Variant report

Variant	rs7925122
Chromosome Location	chr11:663463-663464
allele	C/G
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	SMC3	chr11:662608-663713	SK-N-SH	brain:	n/a	chr11:662880-662890 chr11:662876-662890 chr11:662930-662944
2	MAZ	chr11:662665-663485	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:662818..664389-chr11:748075..750567,2	K562	blood:
2	chr11:649426..653005-chr11:660826..664030,3	K562	blood:

Variant related genes	Relation type
ENSG00000255158	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10751661	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10902189	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10902194	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.82[ASN][1000 genomes]
rs11246240	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11246241	0.83[ASN][1000 genomes]
rs11246244	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11246248	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11246267	0.82[ASN][1000 genomes]
rs11822917	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366210	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12575488	0.86[ASN][1000 genomes]
rs28594998	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4074376	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]
rs4074979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4331145	0.85[CHB][hapmap]
rs4963172	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6598000	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6598001	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6598002	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6598004	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6598005	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7102376	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7116535	0.80[ASN][1000 genomes]
rs7116631	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.80[ASN][1000 genomes]
rs7118095	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.82[ASN][1000 genomes]
rs7121608	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7123677	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.82[ASN][1000 genomes]
rs7126455	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.80[ASN][1000 genomes]
rs7128243	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.82[ASN][1000 genomes]
rs73407113	0.82[ASN][1000 genomes]
rs73407114	0.82[ASN][1000 genomes]
rs73407117	0.82[ASN][1000 genomes]
rs752306	0.92[CHB][hapmap]
rs7925259	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7927761	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7930365	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7933080	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935419	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7937061	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941038	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7943527	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7948371	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7949932	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951023	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9734266	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	nsv1051547	chr11:651993-766633	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
24	nsv1053342	chr11:653154-780756	Flanking Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
25	nsv540881	chr11:653154-780756	Flanking Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
26	esv3363507	chr11:663352-666150	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
27	esv3432649	chr11:663352-666150	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7925122	TMEM80	cis	Artery Tibial	GTEx
rs7925122	TMEM80	cis	brain	seeQTL
rs7925122	TMEM80	cis	lung	GTEx
rs7925122	TMEM80	cis	Nerve Tibial	GTEx
rs7925122	TMEM80	cis	multi-tissue	Pritchard
rs7925122	TMEM80	cis	Adipose Subcutaneous	GTEx
rs7925122	TMEM80	cis	lymphoblastoid	seeQTL
rs7925122	TMEM80	cis	Lymphoblastoid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:639800-665600	Weak transcription	Psoas Muscle	Psoas
2	chr11:639800-673800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr11:640400-670600	Strong transcription	Dnd41	blood
4	chr11:640800-680800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr11:641200-665200	Weak transcription	HSMM	muscle
6	chr11:641200-673800	Weak transcription	HUVEC	blood vessel
7	chr11:641600-664000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr11:642400-665600	Weak transcription	Osteobl	bone
9	chr11:643000-664200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:643000-665400	Weak transcription	Hela-S3	cervix
11	chr11:643000-665600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr11:643000-673800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:646800-665600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr11:647000-664200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:647000-665800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr11:648200-667600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:650200-672200	Weak transcription	NH-A	brain
18	chr11:650800-664400	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr11:652400-664200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr11:652600-664000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr11:653000-663600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr11:653000-691200	Weak transcription	Fetal Brain Male	brain
23	chr11:653200-664200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr11:653200-669400	Strong transcription	Thymus	Thymus
25	chr11:653400-668000	Strong transcription	Fetal Brain Female	brain
26	chr11:653800-664200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr11:654000-665200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr11:654000-676800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr11:654200-665000	Weak transcription	Primary B cells from cord blood	blood
30	chr11:654400-664200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr11:655000-664200	Strong transcription	Fetal Thymus	thymus
32	chr11:655000-669000	Strong transcription	Primary T cells from cord blood	blood
33	chr11:655400-663800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:656000-664000	Strong transcription	NHLF	lung
35	chr11:656200-664000	Strong transcription	Esophagus	oesophagus
36	chr11:656200-667400	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr11:656600-663800	Strong transcription	Lung	lung
38	chr11:656600-664000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr11:656600-664000	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr11:656600-667200	Strong transcription	Brain Germinal Matrix	brain
41	chr11:656800-664000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr11:657200-664000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr11:657400-672000	Weak transcription	Small Intestine	intestine
44	chr11:657800-672200	Weak transcription	Brain Angular Gyrus	brain
45	chr11:658200-663600	Strong transcription	A549	lung
46	chr11:658200-665200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr11:658400-665200	Weak transcription	HSMMtube	muscle
48	chr11:658600-665400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr11:658800-663600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr11:659000-682200	Strong transcription	Fetal Intestine Small	intestine

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