Variant report

Variant	rs4074376
Chromosome Location	chr11:648715-648716
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:648618-648736	MCF-7	breast:	n/a	n/a
2	POLR2A	chr11:648503-648741	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:643825..646244-chr11:647527..650407,2	MCF-7	breast:
2	chr11:647489..650784-chr11:651694..654535,3	MCF-7	breast:
3	chr11:554952..557594-chr11:648539..650525,2	K562	blood:

Variant related genes	Relation type
DEAF1	TF binding region
ENSG00000185522	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10902189	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10902194	0.82[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs11246240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11246241	0.82[ASN][1000 genomes]
rs11246244	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11246248	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11822917	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12366210	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12575488	0.81[ASN][1000 genomes]
rs28594998	0.89[ASN][1000 genomes]
rs4074979	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4963172	0.89[ASN][1000 genomes]
rs6598000	0.91[ASN][1000 genomes]
rs6598001	0.90[ASN][1000 genomes]
rs6598002	0.92[ASN][1000 genomes]
rs6598004	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6598005	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7102376	0.89[ASN][1000 genomes]
rs7116535	0.80[EUR][1000 genomes]
rs7116631	0.82[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7118095	0.82[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7121608	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs7123677	0.82[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7126455	0.82[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7128243	0.82[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs752306	0.84[CHB][hapmap]
rs7925122	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7925259	0.91[ASN][1000 genomes]
rs7927761	0.94[ASN][1000 genomes]
rs7930365	0.92[ASN][1000 genomes]
rs7933080	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7935419	0.91[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7937061	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7941038	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7943527	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7949932	0.92[ASN][1000 genomes]
rs7951023	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9734266	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:36 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046476	chr11:205983-911945	Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	260 gene(s)	inside rSNPs	diseases
2	nsv896478	chr11:350917-888632	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	234 gene(s)	inside rSNPs	diseases
3	nsv896479	chr11:350917-934594	Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
4	nsv896485	chr11:353757-656845	Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	167 gene(s)	inside rSNPs	diseases
5	nsv896486	chr11:353757-662407	ZNF genes & repeats Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	169 gene(s)	inside rSNPs	diseases
6	nsv896487	chr11:353757-888632	Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	234 gene(s)	inside rSNPs	diseases
7	nsv896506	chr11:378188-715420	Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
8	nsv469923	chr11:378188-1323564	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	248 gene(s)	inside rSNPs	diseases
9	nsv896511	chr11:385442-715420	Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	162 gene(s)	inside rSNPs	diseases
10	esv2758250	chr11:409846-1357392	Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
11	esv2759794	chr11:409846-1357392	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
12	nsv1053964	chr11:491334-692433	Active TSS Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	138 gene(s)	inside rSNPs	diseases
13	nsv896545	chr11:521302-710558	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	129 gene(s)	inside rSNPs	diseases
14	nsv1039558	chr11:534242-672091	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	124 gene(s)	inside rSNPs	diseases
15	nsv896550	chr11:551405-662407	Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	118 gene(s)	inside rSNPs	diseases
16	nsv896551	chr11:551405-888632	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
17	nsv1053653	chr11:553925-697511	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	123 gene(s)	inside rSNPs	diseases
18	nsv540879	chr11:553925-697511	Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	123 gene(s)	inside rSNPs	diseases
19	nsv467635	chr11:557342-656845	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	116 gene(s)	inside rSNPs	diseases
20	nsv552858	chr11:557342-656845	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	116 gene(s)	inside rSNPs	diseases
21	nsv552859	chr11:557342-656940	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	116 gene(s)	inside rSNPs	diseases
22	nsv896561	chr11:564295-662407	Flanking Active TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	110 gene(s)	inside rSNPs	diseases
23	nsv552861	chr11:589246-662407	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
24	nsv896562	chr11:589564-662407	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
25	nsv896563	chr11:589564-888632	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
26	nsv896564	chr11:594264-656845	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
27	nsv896565	chr11:598033-662407	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
28	esv2762889	chr11:606294-653614	Genic enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
29	nsv896567	chr11:607050-656523	ZNF genes & repeats Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
30	nsv896570	chr11:620599-715420	Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
31	nsv832043	chr11:631027-758602	Strong transcription Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
32	nsv1049093	chr11:638768-884107	Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
33	nsv540880	chr11:638768-884107	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
34	nsv972894	chr11:646542-662439	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
35	nsv552867	chr11:647869-688312	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
36	nsv552868	chr11:648045-683403	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4074376	TMEM80	cis	Nerve Tibial	GTEx
rs4074376	TMEM80	cis	lymphoblastoid	seeQTL
rs4074376	TMEM80	cis	Artery Tibial	GTEx
rs4074376	TMEM80	Cis_1M	lymphoblastoid	RTeQTL
rs4074376	TMEM80	cis	lung	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:639400-650800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr11:639400-655200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr11:639800-665600	Weak transcription	Psoas Muscle	Psoas
4	chr11:639800-673800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr11:640400-670600	Strong transcription	Dnd41	blood
6	chr11:640800-650800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr11:640800-680800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr11:641000-650000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:641000-653200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr11:641000-653600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr11:641200-650800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr11:641200-651800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr11:641200-653200	Weak transcription	HSMMtube	muscle
14	chr11:641200-658400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:641200-665200	Weak transcription	HSMM	muscle
16	chr11:641200-673800	Weak transcription	HUVEC	blood vessel
17	chr11:641400-652200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr11:641400-653400	Weak transcription	Fetal Lung	lung
19	chr11:641400-660600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr11:641600-650600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr11:641600-650600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr11:641600-651600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr11:641600-664000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr11:642400-665600	Weak transcription	Osteobl	bone
25	chr11:642800-649600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr11:643000-648800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr11:643000-648800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr11:643000-650400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr11:643000-650600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr11:643000-650800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr11:643000-651400	Weak transcription	K562	blood
32	chr11:643000-653800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr11:643000-654600	Weak transcription	Stomach Mucosa	stomach
34	chr11:643000-656600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr11:643000-657600	Weak transcription	HMEC	breast
36	chr11:643000-657800	Weak transcription	NHDF-Ad	bronchial
37	chr11:643000-660400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr11:643000-662800	Strong transcription	Fetal Stomach	stomach
39	chr11:643000-663000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr11:643000-663400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:643000-664200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr11:643000-665400	Weak transcription	Hela-S3	cervix
43	chr11:643000-665600	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr11:643000-673800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr11:644000-659600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr11:644200-657400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr11:644200-658400	Weak transcription	NHEK	skin
48	chr11:644600-649600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr11:644600-649600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr11:644600-650600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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