Variant report

Variant	rs1581240
Chromosome Location	chr10:93801585-93801586
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10509640	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10786026	1.00[JPT][hapmap]
rs10882019	0.84[JPT][hapmap]
rs1104012	0.80[JPT][hapmap]
rs11186744	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11817194	1.00[JPT][hapmap]
rs12251446	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12253972	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12254369	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12256118	0.84[JPT][hapmap]
rs12263532	1.00[JPT][hapmap]
rs12263639	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12266974	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12267763	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17107211	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17107472	0.84[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap]
rs1711850	0.84[JPT][hapmap]
rs1935864	0.84[JPT][hapmap];0.85[MEX][hapmap]
rs2048901	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2252200	1.00[JPT][hapmap]
rs2676824	1.00[JPT][hapmap]
rs2792019	1.00[JPT][hapmap]
rs4509678	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4642987	1.00[JPT][hapmap]
rs55737168	0.86[AMR][1000 genomes]
rs6583801	0.84[JPT][hapmap]
rs7070076	1.00[JPT][hapmap]
rs7071659	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7077506	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7901434	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7904900	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7909870	1.00[JPT][hapmap]
rs7911552	1.00[JPT][hapmap]
rs7912721	0.94[JPT][hapmap]
rs7915659	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7924014	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs833364	0.84[JPT][hapmap]
rs833365	0.84[JPT][hapmap]
rs833368	1.00[JPT][hapmap]
rs833380	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051226	chr10:93711296-93915586	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv540745	chr10:93711296-93915586	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1042818	chr10:93715483-93855032	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv895893	chr10:93747260-93875264	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1581240	BTAF1	cis	multi-tissue	Pritchard

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93704800-93807400	Weak transcription	Gastric	stomach
2	chr10:93774600-93805200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr10:93785400-93802000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:93785800-93807600	Weak transcription	Pancreas	Pancrea
5	chr10:93786600-93807800	Weak transcription	Fetal Heart	heart
6	chr10:93786800-93804800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:93786800-93807600	Weak transcription	Aorta	Aorta
8	chr10:93787200-93805400	Weak transcription	Right Ventricle	heart
9	chr10:93787200-93812200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr10:93787400-93807600	Weak transcription	Spleen	Spleen
11	chr10:93787400-93811200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr10:93787400-93818400	Weak transcription	Colonic Mucosa	Colon
13	chr10:93787400-93840000	Weak transcription	Small Intestine	intestine
14	chr10:93787600-93828000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr10:93788000-93812000	Weak transcription	Brain Anterior Caudate	brain
16	chr10:93788200-93804200	Weak transcription	NHLF	lung
17	chr10:93788400-93814200	Weak transcription	HepG2	liver
18	chr10:93789800-93816400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr10:93791800-93838400	Weak transcription	Brain Substantia Nigra	brain
20	chr10:93792000-93805200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr10:93792200-93805400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr10:93792200-93807600	Weak transcription	Left Ventricle	heart
23	chr10:93792400-93809600	Weak transcription	NHEK	skin
24	chr10:93792400-93814800	Weak transcription	Hela-S3	cervix
25	chr10:93792600-93807600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr10:93792800-93807800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr10:93792800-93837800	Weak transcription	Brain Angular Gyrus	brain
28	chr10:93793000-93807600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr10:93793000-93814600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr10:93793200-93812000	Weak transcription	Brain Hippocampus Middle	brain
31	chr10:93793200-93812400	Weak transcription	Placenta	Placenta
32	chr10:93793600-93805000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr10:93793600-93805400	Weak transcription	Lung	lung
34	chr10:93793600-93807600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr10:93793800-93802000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr10:93793800-93802400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr10:93793800-93804400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr10:93793800-93805200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr10:93793800-93807600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr10:93793800-93811400	Weak transcription	Ovary	ovary
41	chr10:93794000-93807600	Weak transcription	Primary B cells from cord blood	blood
42	chr10:93794200-93810800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr10:93794200-93811400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr10:93794200-93811400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr10:93794200-93811600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr10:93794400-93802200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr10:93794400-93804600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr10:93794400-93806200	Weak transcription	Liver	Liver
49	chr10:93794400-93812400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr10:93794400-93814200	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links