Variant report

Variant	rs7123677
Chromosome Location	chr11:688804-688805
allele	A/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	POLR2A	chr11:688671-689165	HL-60	blood:	n/a	n/a
2	POLR2A	chr11:688602-689174	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:687189..689828-chr11:788717..791634,2	K562	blood:
2	chr11:682586..685184-chr11:687662..690609,3	K562	blood:
3	chr11:688501..691932-chr11:692980..697337,6	MCF-7	breast:

Variant related genes	Relation type
DEAF1	TF binding region
ENSG00000177042	Chromatin interaction
ENSG00000177106	Chromatin interaction
ENSG00000177030	Chromatin interaction
ENSG00000184524	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10751661	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10902189	0.82[ASN][1000 genomes]
rs10902194	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11246240	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11246244	0.80[ASN][1000 genomes]
rs11246248	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11246267	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11246269	0.81[AFR][1000 genomes]
rs11822917	0.82[ASN][1000 genomes]
rs4074376	0.82[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs4074979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4331145	0.85[CHB][hapmap]
rs6598000	0.81[ASN][1000 genomes]
rs6598001	0.80[ASN][1000 genomes]
rs6598002	0.82[ASN][1000 genomes]
rs6598004	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]
rs6598005	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7116631	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7118095	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7121478	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7121608	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7126455	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7128243	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73407113	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73407114	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73407117	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs752306	0.92[CHB][hapmap]
rs7925122	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]
rs7925259	0.81[ASN][1000 genomes]
rs7927761	0.80[ASN][1000 genomes]
rs7928305	0.88[ASN][1000 genomes]
rs7928943	0.82[AFR][1000 genomes]
rs7930365	0.82[ASN][1000 genomes]
rs7933080	0.82[ASN][1000 genomes]
rs7935419	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7937061	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7941038	0.82[ASN][1000 genomes]
rs7943527	0.82[ASN][1000 genomes]
rs7945422	0.83[ASN][1000 genomes]
rs7949932	0.82[ASN][1000 genomes]
rs7951023	0.80[ASN][1000 genomes]
rs9734224	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9734266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	nsv896573	chr11:688312-702097	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
24	nsv896574	chr11:688312-755659	Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
25	nsv896575	chr11:688312-840319	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
26	nsv896576	chr11:688312-870446	Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
27	nsv896577	chr11:688312-888632	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7123677	TMEM80	cis	Esophagus Muscularis	GTEx
rs7123677	TMEM80	cis	lung	GTEx
rs7123677	TMEM80	cis	Nerve Tibial	GTEx
rs7123677	TMEM80	cis	lymphoblastoid	seeQTL
rs7123677	TMEM80	cis	brain	seeQTL
rs7123677	TMEM80	cis	Lymphoblastoid	GTEx
rs7123677	TMEM80	cis	Cerebellum	GTEx
rs7123677	TMEM80	cis	multi-tissue	Pritchard
rs7123677	TMEM80	cis	Adipose Subcutaneous	GTEx
rs7123677	TMEM80	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:653000-691200	Weak transcription	Fetal Brain Male	brain
2	chr11:659000-693400	Weak transcription	Stomach Mucosa	stomach
3	chr11:662000-693000	Weak transcription	Fetal Heart	heart
4	chr11:665000-689400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr11:665000-691600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr11:665200-691200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:666200-693400	Weak transcription	Right Atrium	heart
8	chr11:666600-692000	Strong transcription	Fetal Stomach	stomach
9	chr11:669200-691600	Strong transcription	Fetal Brain Female	brain
10	chr11:669200-692200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr11:670000-690400	Strong transcription	Fetal Muscle Leg	muscle
12	chr11:670400-690800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:670600-691400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:671400-690200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr11:671400-691200	Strong transcription	Fetal Muscle Trunk	muscle
16	chr11:671400-691200	Strong transcription	Dnd41	blood
17	chr11:671600-689600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr11:671600-691400	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr11:671800-692000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr11:672000-691000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:673200-691800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:673200-692000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr11:673400-690000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:673400-690200	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr11:673400-691600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:673600-689600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr11:673600-690200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr11:674600-690800	Weak transcription	Fetal Kidney	kidney
29	chr11:674800-690800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr11:676800-690200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr11:676800-691400	Strong transcription	Brain Germinal Matrix	brain
32	chr11:677800-689600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr11:677800-690200	Strong transcription	Duodenum Mucosa	Duodenum
34	chr11:678000-690000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:678000-690000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr11:678000-690200	Strong transcription	Fetal Intestine Large	intestine
37	chr11:678000-690400	Strong transcription	Lung	lung
38	chr11:678200-690000	Strong transcription	Esophagus	oesophagus
39	chr11:678200-690000	Strong transcription	HepG2	liver
40	chr11:678200-690400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr11:678200-691200	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr11:678200-691400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr11:678400-689000	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr11:678400-691600	Strong transcription	NHLF	lung
45	chr11:678600-691400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr11:679600-693600	Weak transcription	Small Intestine	intestine
47	chr11:680200-694800	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr11:680800-689200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
49	chr11:680800-689600	Strong transcription	Fetal Lung	lung
50	chr11:680800-691000	Strong transcription	Spleen	Spleen

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