Variant report

Variant	rs4717980
Chromosome Location	chr7:63542866-63542867
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10238902	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs10252057	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10479701	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10949869	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs10949870	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10949871	0.81[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs10949873	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10949875	0.92[EUR][1000 genomes]
rs11760975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11769287	0.88[ASW][hapmap];0.87[CEU][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap]
rs11770663	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11772251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11773874	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11979814	0.87[CEU][hapmap];0.83[YRI][hapmap]
rs12530603	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12531199	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12535845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13221374	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13222343	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13224398	0.84[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs13230517	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13240248	0.95[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1595621	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1816700	0.95[CEU][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1837336	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1837337	0.84[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1837338	1.00[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.83[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1837339	0.84[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1837340	0.81[EUR][1000 genomes]
rs1946853	0.82[ASW][hapmap];0.86[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap]
rs1972857	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2008969	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2014900	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2060420	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2060421	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2083286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2118859	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2861506	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2861507	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2861509	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2861510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2861511	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34705196	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4301347	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4349869	0.84[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4570020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4717167	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4717168	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4717170	0.86[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4717171	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4717969	0.87[CEU][hapmap];0.82[YRI][hapmap]
rs4717978	0.91[CEU][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4717979	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4717981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4717982	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4717986	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5005469	0.92[EUR][1000 genomes]
rs6460115	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6460116	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6948848	0.92[EUR][1000 genomes]
rs6953268	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6958588	0.95[CEU][hapmap];0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs6962663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs6973547	0.87[CEU][hapmap]
rs6974169	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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6975336	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6975985	0.88[ASW][hapmap];0.87[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap]
rs6976585	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6979641	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7778793	0.96[CEU][hapmap];0.84[CHB][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7785462	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7787614	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7791554	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7797492	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7797531	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7797838	0.91[EUR][1000 genomes]
rs7800439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7800540	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7807146	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7808723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs893623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9647796	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9647797	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs978661	0.84[CHB][hapmap]
rs978662	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv888255	chr7:63175168-63990100	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
2	nsv534361	chr7:63328472-63955286	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv888259	chr7:63363001-64009193	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	esv3365963	chr7:63367092-63587809	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	esv3496812	chr7:63367459-63649196	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	esv3496813	chr7:63367459-63649196	Weak transcription ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	esv3336155	chr7:63368772-63650552	Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv464514	chr7:63383123-63847894	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
9	nsv607304	chr7:63383123-63847894	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
10	nsv888260	chr7:63389550-63565953	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1016151	chr7:63420068-63704289	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv1019447	chr7:63420068-63766444	Active TSS ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
13	nsv1016466	chr7:63438466-63969492	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
14	nsv888263	chr7:63464342-63565953	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	esv3378509	chr7:63482728-63739475	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
16	nsv607305	chr7:63502629-63783386	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
17	nsv1019217	chr7:63520745-63802106	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
18	nsv607306	chr7:63525863-63761081	ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
19	nsv888264	chr7:63526245-63791269	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
20	nsv981494	chr7:63526308-63584018	ZNF genes & repeats Weak transcription Active TSS Strong transcription	TF binding region CpG island lncRNA	12 gene(s)	inside rSNPs	diseases
21	nsv948798	chr7:63533811-63751201	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
22	nsv1016645	chr7:63533811-63784883	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
23	nsv1019909	chr7:63533811-63791269	Genic enhancers Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
24	nsv1027639	chr7:63536201-63791269	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
25	nsv607307	chr7:63537173-63783386	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4717980	SNORA22	cis	parietal	SCAN
rs4717980	CRCP	cis	parietal	SCAN
rs4717980	ZNF117	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:63524000-63544200	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr7:63528600-63544200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr7:63529600-63544000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
4	chr7:63532600-63544000	ZNF genes & repeats	Brain Angular Gyrus	brain
5	chr7:63532600-63544000	ZNF genes & repeats	Brain Substantia Nigra	brain
6	chr7:63533600-63543400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:63534000-63544000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
8	chr7:63534200-63544000	ZNF genes & repeats	Liver	Liver
9	chr7:63535600-63544200	ZNF genes & repeats	Brain Anterior Caudate	brain
10	chr7:63535800-63543400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
11	chr7:63535800-63544000	ZNF genes & repeats	Brain Cingulate Gyrus	brain
12	chr7:63535800-63544000	ZNF genes & repeats	Brain Hippocampus Middle	brain
13	chr7:63535800-63544000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
14	chr7:63537200-63543800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
15	chr7:63540400-63544200	ZNF genes & repeats	Ovary	ovary
16	chr7:63541200-63544000	ZNF genes & repeats	Left Ventricle	heart
17	chr7:63541200-63544000	ZNF genes & repeats	Dnd41	blood
18	chr7:63541200-63544200	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
19	chr7:63541200-63544200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
20	chr7:63541400-63544000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
21	chr7:63541400-63544200	ZNF genes & repeats	Aorta	Aorta
22	chr7:63541400-63544200	ZNF genes & repeats	Pancreas	Pancrea
23	chr7:63541600-63544200	ZNF genes & repeats	Lung	lung
24	chr7:63542600-63543600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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