Variant report

Variant	rs3962875
Chromosome Location	chr1:77753122-77753123
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10493536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10493537	0.88[AMR][1000 genomes]
rs10493602	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10873932	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11162312	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11162317	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11162319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1167198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1167205	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.85[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12057706	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12059542	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12061595	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12062754	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs12070404	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12070567	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs12071077	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12072100	0.80[ASN][1000 genomes]
rs12076479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12079185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12079206	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12079234	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12079316	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12088702	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12089562	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12097728	0.80[ASN][1000 genomes]
rs1502526	0.82[CEU][hapmap]
rs1615404	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1616272	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1670611	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1670612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1670614	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1670617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1670618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17098286	1.00[TSI][hapmap]
rs17099885	1.00[ASW][hapmap];0.82[CEU][hapmap]
rs17099982	0.82[CEU][hapmap]
rs17099983	1.00[ASW][hapmap];0.82[CEU][hapmap]
rs17099986	0.82[CEU][hapmap]
rs17100001	0.82[CEU][hapmap]
rs17100002	0.82[CEU][hapmap]
rs17100005	0.82[CEU][hapmap]
rs17100021	0.82[CEU][hapmap]
rs17100075	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs17100133	0.88[AMR][1000 genomes]
rs17100172	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17100185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17100198	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17100204	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17100317	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17100319	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17100422	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs17100440	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs1721163	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1721164	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1721165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1721168	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1779177	0.81[CHB][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1779178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1779180	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1779181	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1966873	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2054017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2054018	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2054019	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2154090	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2602953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2799551	0.96[ASN][1000 genomes]
rs2799552	0.85[ASN][1000 genomes]
rs2799553	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2815313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28476720	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28605112	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2996486	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4033035	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4033036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4033037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41292262	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949653	0.92[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs60401394	0.80[ASN][1000 genomes]
rs6661765	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6665543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668328	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6669724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685087	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6691415	0.84[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs6693999	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6698996	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6703688	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs721514	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[MKK][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72677859	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72677889	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72679506	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72679513	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72679514	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72679531	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72679538	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72679540	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72679542	0.84[EUR][1000 genomes]
rs7367731	0.81[ASN][1000 genomes]
rs7511768	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7517796	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529083	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7531431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537603	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7545096	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3962875	PIGK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77749000-77779200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:77749200-77754800	Weak transcription	HSMMtube	muscle
3	chr1:77749200-77778400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:77749400-77754600	Weak transcription	Osteobl	bone
5	chr1:77749400-77755600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:77749400-77781600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:77749800-77754000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:77749800-77768800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:77750000-77753800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:77750000-77753800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:77750000-77757400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:77750200-77753400	Weak transcription	Primary T cells from cord blood	blood
13	chr1:77750400-77754000	Weak transcription	Brain Angular Gyrus	brain
14	chr1:77750600-77753400	Enhancers	Brain Substantia Nigra	brain
15	chr1:77750600-77754400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:77750600-77772400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr1:77750800-77753200	Weak transcription	Brain Anterior Caudate	brain
18	chr1:77750800-77768200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:77751000-77757400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:77751000-77767600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:77751200-77754000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:77751200-77757800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:77751400-77754600	Weak transcription	NHLF	lung
24	chr1:77751400-77764600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:77751600-77753800	Weak transcription	HUVEC	blood vessel
26	chr1:77752200-77756400	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:77752600-77753400	Strong transcription	NHDF-Ad	bronchial
28	chr1:77752600-77757200	Strong transcription	HSMM	muscle

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