Variant report

Variant	rs3924661
Chromosome Location	chr10:4929527-4929528
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10751986	0.86[AFR][1000 genomes]
rs10751987	0.92[AFR][1000 genomes]
rs10751990	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10795202	0.80[GIH][hapmap];0.88[LWK][hapmap];0.89[MKK][hapmap];0.88[YRI][hapmap]
rs10904361	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10904364	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2123353	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs2167702	0.89[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.84[YRI][hapmap]
rs4242775	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4242776	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4242777	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4242778	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4242779	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4266965	0.83[ASW][hapmap];0.85[CEU][hapmap];0.97[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4295949	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4304654	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4363494	0.90[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap]
rs4406725	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4460716	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4488090	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4520487	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4534472	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4540749	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4543886	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4545440	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4564222	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4880690	0.88[YRI][hapmap]
rs4880699	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4880700	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4881366	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4881368	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7071039	0.87[AFR][1000 genomes]
rs7071257	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7089338	0.82[MEX][hapmap]
rs7089546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7092190	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7095641	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7906540	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7906576	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7910287	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7918169	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7922213	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894792	chr10:4832920-5498724	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv948794	chr10:4863093-5227382	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1045155	chr10:4872239-5211318	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040343	chr10:4872814-5196815	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540462	chr10:4872814-5196815	Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv869470	chr10:4878904-5203685	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv466713	chr10:4901798-5319679	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv549881	chr10:4901798-5319679	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv1042940	chr10:4916614-4974581	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv947581	chr10:4925629-4933637	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1050246	chr10:4927428-5211318	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3924661	AKR1E2	cis	cerebellum	SCAN
rs3924661	AKR1E2	cis	parietal	SCAN
rs3924661	AKR1C1	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:4908800-4944200	Weak transcription	Adipose Nuclei	Adipose
2	chr10:4910400-4936400	Weak transcription	Left Ventricle	heart
3	chr10:4915800-4943600	Weak transcription	Aorta	Aorta
4	chr10:4916800-4936400	Weak transcription	Pancreas	Pancrea
5	chr10:4918400-4968000	Weak transcription	Primary T cells from cord blood	blood
6	chr10:4918800-4931400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr10:4919200-4936800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr10:4921600-4930800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr10:4924800-4929600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr10:4925600-4930200	Strong transcription	Liver	Liver
11	chr10:4925800-4936400	Weak transcription	Right Atrium	heart
12	chr10:4926000-4929800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr10:4926200-4931400	Weak transcription	HepG2	liver
14	chr10:4927400-4930200	Enhancers	Primary hematopoietic stem cells	blood
15	chr10:4927800-4936200	Weak transcription	Lung	lung
16	chr10:4929200-4929800	Enhancers	Primary B cells from peripheral blood	blood
17	chr10:4929200-4930000	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr10:4929200-4930000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr10:4929200-4930200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr10:4929200-4932200	Enhancers	Fetal Stomach	stomach
21	chr10:4929400-4930000	Enhancers	Fetal Muscle Leg	muscle

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