Variant report

Variant	rs17100440
Chromosome Location	chr1:77825996-77825997
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10493536	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs10493602	1.00[CEU][hapmap];0.84[CHB][hapmap];0.80[EUR][1000 genomes]
rs10873932	0.84[EUR][1000 genomes]
rs11162312	0.80[EUR][1000 genomes]
rs11162317	0.84[EUR][1000 genomes]
rs11162319	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1167198	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs1167205	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs12057706	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12059542	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12061595	0.84[EUR][1000 genomes]
rs12062754	0.92[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs12070404	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12070567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12071077	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12072100	0.84[ASN][1000 genomes]
rs12076479	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs12079185	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs12079206	0.80[EUR][1000 genomes]
rs12079234	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs12079316	0.80[EUR][1000 genomes]
rs12088702	0.84[EUR][1000 genomes]
rs12089562	0.84[EUR][1000 genomes]
rs12097728	0.82[ASN][1000 genomes]
rs1615404	0.80[EUR][1000 genomes]
rs1616272	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap]
rs1670611	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1670612	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs1670614	0.80[EUR][1000 genomes]
rs1670617	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs1670618	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs17099982	0.82[CEU][hapmap]
rs17099983	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]
rs17100185	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs17100204	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs17100317	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17100319	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17100422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1721163	0.80[EUR][1000 genomes]
rs1721164	0.80[EUR][1000 genomes]
rs1721165	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs1779177	0.80[EUR][1000 genomes]
rs1779178	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs1779180	0.80[EUR][1000 genomes]
rs1779181	0.80[EUR][1000 genomes]
rs1966873	0.84[EUR][1000 genomes]
rs2054017	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2054018	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2054019	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2154090	0.84[EUR][1000 genomes]
rs2602953	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs2799553	0.84[EUR][1000 genomes]
rs2815313	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes]
rs28476720	0.80[EUR][1000 genomes]
rs28605112	0.80[EUR][1000 genomes]
rs3962875	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs4033035	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs4033036	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs4033037	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.80[EUR][1000 genomes]
rs41292262	0.84[EUR][1000 genomes]
rs4949653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs60401394	0.88[ASN][1000 genomes]
rs6661765	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap]
rs6665543	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.80[EUR][1000 genomes]
rs6668328	0.84[EUR][1000 genomes]
rs6669724	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs6680763	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.80[EUR][1000 genomes]
rs6683829	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap]
rs6685087	0.80[EUR][1000 genomes]
rs6691415	0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs6693999	0.80[EUR][1000 genomes]
rs6698996	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes]
rs6703688	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs721514	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72677859	0.80[EUR][1000 genomes]
rs72677889	0.84[EUR][1000 genomes]
rs72679506	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72679513	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72679514	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72679531	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72679538	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72679540	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72679542	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72679558	0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7367731	0.83[ASN][1000 genomes]
rs7511768	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs7517796	0.80[EUR][1000 genomes]
rs7529083	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7531431	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs7534033	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs7537603	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap]

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	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
4	nsv1003714	chr1:77756861-77949309	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv2764210	chr1:77825478-77838400	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17100440	PIGK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77789000-77831200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:77795000-77836400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:77803400-77839200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:77813800-77834200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:77814400-77835600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:77817400-77834200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:77819800-77826800	Weak transcription	NHDF-Ad	bronchial
8	chr1:77819800-77835600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:77820400-77836400	Weak transcription	Primary T cells from cord blood	blood
10	chr1:77821000-77835600	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:77824400-77836400	Weak transcription	Brain Anterior Caudate	brain
12	chr1:77825400-77826400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr1:77825600-77826000	Enhancers	Brain Cingulate Gyrus	brain
14	chr1:77825600-77826200	Enhancers	HSMMtube	muscle
15	chr1:77825600-77826800	Enhancers	HSMM	muscle
16	chr1:77825800-77826000	Enhancers	Brain Substantia Nigra	brain
17	chr1:77825800-77826200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:77825800-77826400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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