Variant report

Variant	rs7968837
Chromosome Location	chr12:39946354-39946355
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10876886	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs10876972	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs10877100	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11171891	0.84[CEU][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs11171901	0.86[CEU][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs11171923	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11171938	0.88[CEU][hapmap]
rs11172108	0.96[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[EUR][1000 genomes]
rs11172120	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs11172174	0.82[EUR][1000 genomes]
rs11172183	0.86[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap]
rs11172282	0.88[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11172293	0.87[EUR][1000 genomes]
rs11172319	0.85[ASN][1000 genomes]
rs11172320	0.82[ASN][1000 genomes]
rs11172357	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172386	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172392	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172492	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172493	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172526	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172541	0.89[ASN][1000 genomes]
rs11172592	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172625	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172638	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172650	0.90[ASN][1000 genomes]
rs11172661	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11830643	0.88[ASW][hapmap];0.96[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs12228767	0.88[ASW][hapmap];0.96[CEU][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs12230604	0.88[CEU][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs12424345	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs1512936	1.00[JPT][hapmap];0.88[YRI][hapmap]
rs1567739	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs1828653	0.88[CEU][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs2388320	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs3736466	0.84[CEU][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs4284427	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4320988	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4378431	0.86[ASN][1000 genomes]
rs4390378	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4451772	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4466883	0.87[ASN][1000 genomes]
rs4475956	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4492858	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4500523	0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58240943	0.82[EUR][1000 genomes]
rs58613501	0.82[EUR][1000 genomes]
rs60263267	0.82[ASN][1000 genomes]
rs6581187	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581188	0.89[ASN][1000 genomes]
rs7133376	1.00[ASW][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs7137143	0.84[CEU][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs73094410	0.82[EUR][1000 genomes]
rs73096532	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7316073	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7485730	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7962283	1.00[CEU][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs7965222	0.81[EUR][1000 genomes]
rs7974928	0.84[CEU][hapmap]
rs7979444	0.88[CEU][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1037457	chr12:39898349-40245401	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS 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	9 gene(s)	inside rSNPs	diseases
3	nsv541480	chr12:39898349-40245401	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1039645	chr12:39903123-40022029	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv522940	chr12:39946354-39998144	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv469359	chr12:39946354-40034699	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv558591	chr12:39946354-40034699	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv469361	chr12:39946354-40042220	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv558592	chr12:39946354-40042220	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv899014	chr12:39946354-40068896	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Weak 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	2 gene(s)	inside rSNPs	diseases
11	nsv899015	chr12:39946354-40118249	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7968837	KIF21A	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39935400-39946400	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr12:39938800-39951000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr12:39939800-39950800	Weak transcription	Primary T cells from cord blood	blood
4	chr12:39941400-39949600	Weak transcription	Adipose Nuclei	Adipose
5	chr12:39942600-39951600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:39943600-39951400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr12:39944000-39949600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:39945000-39949800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:39945000-39951600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:39945200-39946400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr12:39945800-39949200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:39945800-39950800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:39946000-39947600	Weak transcription	GM12878-XiMat	blood
14	chr12:39946000-39949200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr12:39946000-39951400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:39946200-39952200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links