Variant report

Variant	rs7124400
Chromosome Location	chr11:3648545-3648546
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10742075	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[EUR][1000 genomes]
rs10742076	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs10742077	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[EUR][1000 genomes]
rs10767349	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs10834635	0.84[EUR][1000 genomes]
rs10834658	0.90[EUR][1000 genomes]
rs11028591	0.95[EUR][1000 genomes]
rs11028592	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12275471	0.89[EUR][1000 genomes]
rs12362270	0.96[EUR][1000 genomes]
rs12422185	0.85[AFR][1000 genomes]
rs12798300	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1567922	0.84[CEU][hapmap];0.91[EUR][1000 genomes]
rs16929912	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17173896	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs17173897	0.91[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs2271580	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2271581	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2271585	0.82[MEX][hapmap]
rs2898934	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs4910579	0.86[EUR][1000 genomes]
rs4910855	0.85[EUR][1000 genomes]
rs58014283	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60847407	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6578401	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7104589	0.84[CEU][hapmap];0.96[EUR][1000 genomes]
rs7108612	0.95[EUR][1000 genomes]
rs7109228	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7109345	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7115278	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7115284	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7118405	0.96[EUR][1000 genomes]
rs7123007	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7123156	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs72852291	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73424284	0.96[EUR][1000 genomes]
rs885412	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047763	chr11:2918998-3751029	Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	esv2758252	chr11:3236512-3801429	Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2759796	chr11:3236512-3801429	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2760300	chr11:3416489-3667988	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	esv18699	chr11:3426081-3674989	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv832051	chr11:3523947-3728714	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv467660	chr11:3568044-3660914	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv553140	chr11:3568044-3660914	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv1820972	chr11:3616884-3801429	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	esv1821329	chr11:3616884-3801429	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv832052	chr11:3616884-3801429	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv428247	chr11:3616884-3801429	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv526441	chr11:3626177-3756686	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv976446	chr11:3626480-3648596	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv1046356	chr11:3628837-3774215	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
16	nsv1044345	chr11:3628912-3739222	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
17	nsv540906	chr11:3628912-3739222	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
18	nsv1044419	chr11:3628912-3751029	Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
19	nsv896892	chr11:3632107-3654676	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv1045810	chr11:3635610-3657520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv1052573	chr11:3637802-3665561	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7124400	TRPC2	cis	multi-tissue	Pritchard

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3646600-3648800	Enhancers	Primary hematopoietic stem cells	blood
2	chr11:3647400-3648600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:3647400-3648600	Enhancers	K562	blood
4	chr11:3647800-3648800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr11:3648000-3648600	Enhancers	Fetal Intestine Large	intestine
6	chr11:3648000-3648600	Enhancers	NHDF-Ad	bronchial
7	chr11:3648200-3648600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr11:3648200-3648600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr11:3648200-3648800	Enhancers	Adipose Nuclei	Adipose
10	chr11:3648200-3648800	Enhancers	Fetal Intestine Small	intestine
11	chr11:3648200-3649000	Enhancers	HSMMtube	muscle
12	chr11:3648200-3656200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr11:3648400-3648600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr11:3648400-3648600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr11:3648400-3648600	Enhancers	Right Atrium	heart

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