Variant report

Variant	rs17711722
Chromosome Location	chr7:65271197-65271198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10807697	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap]
rs11763003	0.85[EUR][1000 genomes]
rs11763147	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs11770828	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs1829942	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1829943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1917563	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs2008188	0.82[YRI][hapmap]
rs2690442	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs34973832	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs35850374	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs4512285	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs4717271	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6960048	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap]
rs736270	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7784623	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs7791814	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs781143	0.96[CEU][hapmap]
rs9530	0.96[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517778	chr7:64462326-65326821	ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv429767	chr7:64473713-65415647	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv917231	chr7:64478253-65300317	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1029796	chr7:64494934-65302696	Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	esv3339156	chr7:64510176-65349050	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	esv2759534	chr7:64551274-65373851	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv427788	chr7:64551274-65390424	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
8	esv2764020	chr7:64594065-65351820	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
9	nsv1018447	chr7:64609892-65308719	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv538897	chr7:64609892-65308719	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv1029942	chr7:64679680-65371565	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
12	nsv538903	chr7:64679680-65371565	Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
13	nsv1019667	chr7:64679680-65380603	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
14	esv2757227	chr7:64694241-65373851	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
15	nsv1025207	chr7:65092426-65339879	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
16	nsv1033400	chr7:65092426-65339879	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
17	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
18	nsv1020622	chr7:65161364-65339879	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Calcium levels	24068962	GWAS catalog

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs17711722	ERV3	cis	cerebellum	SCAN
rs17711722	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs17711722	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs17711722	RP4-756H11.3	cis	lung	GTEx
rs17711722	RP4-756H11.3	cis	Thyroid	GTEx
rs17711722	CRCP	cis	cerebellum	SCAN
rs17711722	ZNF273	cis	cerebellum	SCAN
rs17711722	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs17711722	GUSB	cis	lymphoblastoid	seeQTL
rs17711722	RABGEF1	cis	cerebellum	SCAN
rs17711722	GUSB	cis	cerebellum	SCAN
rs17711722	GUSB	cis	parietal	SCAN
rs17711722	RP4-756H11.3	cis	Artery Aorta	GTEx
rs17711722	CRCP	cis	parietal	SCAN
rs17711722	RP4-756H11.3	cis	Artery Tibial	GTEx
rs17711722	KCTD7	cis	parietal	SCAN
rs17711722	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs17711722	ERV3	cis	parietal	SCAN
rs17711722	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs17711722	RP4-756H11.3	cis	Nerve Tibial	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65236400-65272600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr7:65236400-65273000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:65236600-65273200	Weak transcription	Pancreas	Pancrea
4	chr7:65247800-65303400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr7:65260800-65302600	Weak transcription	Gastric	stomach
6	chr7:65263800-65271400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr7:65263800-65284400	Weak transcription	Spleen	Spleen
8	chr7:65264000-65273800	Weak transcription	Brain Anterior Caudate	brain
9	chr7:65264000-65302600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr7:65264000-65302800	Weak transcription	Esophagus	oesophagus
11	chr7:65264000-65310800	Weak transcription	Fetal Intestine Small	intestine
12	chr7:65264200-65271800	Weak transcription	NHEK	skin
13	chr7:65264200-65292400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr7:65264600-65292800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr7:65265200-65274200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr7:65265400-65272000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:65265600-65304400	Weak transcription	Left Ventricle	heart
18	chr7:65266600-65278800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr7:65266800-65311000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr7:65267600-65304000	Weak transcription	Placenta	Placenta
21	chr7:65268400-65279800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr7:65270200-65271800	Weak transcription	Right Ventricle	heart
23	chr7:65270200-65273000	Weak transcription	Aorta	Aorta
24	chr7:65270200-65282600	Weak transcription	Brain Substantia Nigra	brain
25	chr7:65270200-65286600	Weak transcription	Liver	Liver
26	chr7:65270200-65302800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr7:65270600-65271600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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