Variant report

Variant	rs11265122
Chromosome Location	chr1:154087033-154087034
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1051370	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10559	0.83[ASW][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs10908558	0.95[LWK][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap]
rs10908627	0.91[ASW][hapmap]
rs10908723	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1110165	0.83[ASW][hapmap];0.89[YRI][hapmap]
rs11264680	0.83[ASW][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs11264743	0.95[LWK][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap]
rs11264866	0.91[ASW][hapmap]
rs11264871	0.90[YRI][hapmap]
rs11264873	0.82[YRI][hapmap]
rs11264875	0.83[ASW][hapmap];0.82[YRI][hapmap]
rs11264886	0.82[YRI][hapmap]
rs11264964	0.83[ASW][hapmap];1.00[YRI][hapmap]
rs11264974	0.82[YRI][hapmap]
rs11265049	1.00[YRI][hapmap]
rs11265076	1.00[YRI][hapmap]
rs11265082	0.91[ASW][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs11265099	0.95[LWK][hapmap];0.83[MKK][hapmap]
rs11265299	0.86[JPT][hapmap]
rs11581644	0.83[ASW][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs12021641	0.91[ASW][hapmap];0.87[LWK][hapmap];0.81[MKK][hapmap];0.90[YRI][hapmap]
rs12026475	0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs12048137	0.82[YRI][hapmap]
rs1212352	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs12405309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12408170	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12408458	0.88[CHD][hapmap];0.86[JPT][hapmap];0.85[MKK][hapmap]
rs12564669	0.88[YRI][hapmap]
rs1572788	0.83[ASW][hapmap];0.86[LWK][hapmap];0.83[MKK][hapmap];0.88[YRI][hapmap]
rs3196889	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3748848	0.83[ASW][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs3791187	0.82[LWK][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap]
rs3828076	0.86[JPT][hapmap]
rs4521985	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4845363	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4845597	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs4845600	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4845601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55677228	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58300038	0.81[AFR][1000 genomes]
rs6659053	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6664278	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs6667928	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6671166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6672856	0.83[ASW][hapmap]
rs6673171	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6678826	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs6680140	0.83[ASW][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs6693620	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6701341	0.91[ASW][hapmap]
rs72696227	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7517127	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7521303	1.00[YRI][hapmap]
rs7535778	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7547663	1.00[YRI][hapmap]
rs7552737	0.91[ASW][hapmap];0.91[LWK][hapmap];0.86[MKK][hapmap];0.90[YRI][hapmap]
rs8450	0.83[ASW][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs946682	0.83[ASW][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
7	nsv520398	chr1:154068196-154141908	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv1000153	chr1:154074249-154152417	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11265122	FLG	cis	parietal	SCAN
rs11265122	SLC39A1	cis	cerebellum	SCAN
rs11265122	SPRR2D	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154086600-154087400	Enhancers	Primary T cells fromperipheralblood	blood
2	chr1:154086800-154087600	Enhancers	Primary T cells from cord blood	blood
3	chr1:154086800-154087600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:154086800-154088200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:154086800-154088400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:154087000-154087400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:154087000-154087600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr1:154087000-154087800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:154087000-154087800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr1:154087000-154087800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr1:154087000-154087800	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr1:154087000-154087800	Enhancers	Duodenum Mucosa	Duodenum
13	chr1:154087000-154088000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr1:154087000-154088000	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr1:154087000-154088000	Enhancers	Thymus	Thymus
16	chr1:154087000-154088000	Enhancers	GM12878-XiMat	blood
17	chr1:154087000-154088200	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links