Variant report

Variant	rs631367
Chromosome Location	chr6:80942903-80942904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1040593	0.83[ASN][1000 genomes]
rs1179571	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525046	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12526876	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12527244	0.85[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs12527712	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12528770	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs12529191	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs12530290	0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16891532	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16891545	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4706829	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4706830	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55755254	1.00[ASN][1000 genomes]
rs57913486	1.00[ASN][1000 genomes]
rs57985210	1.00[ASN][1000 genomes]
rs584372	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585506	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587999	0.93[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588009	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs590686	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs595494	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs598234	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59973779	1.00[ASN][1000 genomes]
rs604732	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs610946	0.93[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612208	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613577	0.93[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623085	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs627968	0.93[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs631314	0.85[EUR][1000 genomes]
rs634499	0.93[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636499	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638921	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640568	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641229	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs642943	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644666	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6454149	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs646369	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs649148	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs651065	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs652576	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs66518170	1.00[ASN][1000 genomes]
rs66560352	1.00[ASN][1000 genomes]
rs66606872	0.86[ASN][1000 genomes]
rs669420	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs670119	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs670390	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs671614	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67379633	1.00[ASN][1000 genomes]
rs67456645	1.00[ASN][1000 genomes]
rs67597629	1.00[ASN][1000 genomes]
rs67632695	1.00[ASN][1000 genomes]
rs677134	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67851250	1.00[ASN][1000 genomes]
rs67988458	1.00[ASN][1000 genomes]
rs685902	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs687702	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs688442	0.93[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906403	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908084	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920430	0.83[ASN][1000 genomes]
rs6924011	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs723308	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72892417	1.00[ASN][1000 genomes]
rs72892426	1.00[ASN][1000 genomes]
rs72892441	1.00[ASN][1000 genomes]
rs72892456	1.00[ASN][1000 genomes]
rs72892458	1.00[ASN][1000 genomes]
rs72908809	1.00[ASN][1000 genomes]
rs72908854	1.00[ASN][1000 genomes]
rs73479994	1.00[ASN][1000 genomes]
rs764442	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7755034	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7757610	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7771047	1.00[JPT][hapmap]
rs7771726	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7772483	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs806781	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs806839	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs806841	1.00[JPT][hapmap]
rs806844	0.83[ASN][1000 genomes]
rs806846	1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs806850	0.83[ASN][1000 genomes]
rs811567	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs932463	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9443739	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9688524	1.00[ASN][1000 genomes]
rs9688535	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830708	chr6:80844283-80996876	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1034096	chr6:80856135-81150170	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv886309	chr6:80880138-80959885	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv886310	chr6:80880138-81025879	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv932996	chr6:80880896-81134991	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv497995	chr6:80883701-81134991	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1033452	chr6:80888667-81000213	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs631367	PHIP	cis	parietal	SCAN
rs631367	PHIP	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80896400-80943800	Weak transcription	Right Ventricle	heart
2	chr6:80914600-80980400	Weak transcription	Ovary	ovary
3	chr6:80915800-80956000	Weak transcription	Brain Substantia Nigra	brain
4	chr6:80920800-80943600	Weak transcription	Psoas Muscle	Psoas
5	chr6:80920800-80953800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:80921400-80973200	Weak transcription	Primary B cells from cord blood	blood
7	chr6:80922200-80964200	Weak transcription	Fetal Intestine Small	intestine
8	chr6:80924000-80968400	Weak transcription	Gastric	stomach
9	chr6:80924000-80976000	Weak transcription	HSMM	muscle
10	chr6:80927800-80959800	Weak transcription	Aorta	Aorta
11	chr6:80929400-80969200	Weak transcription	Left Ventricle	heart
12	chr6:80932800-80956200	Weak transcription	Lung	lung
13	chr6:80933600-80943800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:80935000-80943600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:80936600-80943600	Weak transcription	Pancreas	Pancrea
16	chr6:80936800-80943800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr6:80938000-80956800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:80938600-80952800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:80939000-80974800	Weak transcription	Primary T cells from cord blood	blood
20	chr6:80939200-80959600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:80940600-80964200	Weak transcription	Liver	Liver
22	chr6:80940800-80943600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:80942800-80943200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:80942800-80945800	Enhancers	Fetal Heart	heart

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