Variant report

Variant	rs2870246
Chromosome Location	chr4:91234498-91234499
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10004546	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs11947703	0.83[LWK][hapmap]
rs12642077	0.83[CHB][hapmap]
rs13103126	0.85[CHB][hapmap]
rs1367568	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs1367569	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs1461741	0.85[CHB][hapmap]
rs1461743	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1466391	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17227797	0.85[CHB][hapmap]
rs1835526	0.88[CEU][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap]
rs1870795	0.85[CHB][hapmap]
rs1903579	0.85[CHB][hapmap]
rs1988337	0.85[CHB][hapmap]
rs2116123	0.88[CEU][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs2169399	0.85[CHB][hapmap]
rs4353865	0.85[CHB][hapmap]
rs4694022	0.85[CHB][hapmap]
rs4694023	0.85[CHB][hapmap]
rs6532217	0.88[CEU][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs6813228	0.80[LWK][hapmap]
rs6818163	0.88[CEU][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs6823501	0.88[JPT][hapmap]
rs6831098	0.80[LWK][hapmap]
rs6835114	0.85[CHB][hapmap]
rs6840859	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs6840905	0.83[CEU][hapmap];0.87[TSI][hapmap]
rs6847487	0.88[CEU][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs6854353	0.85[CHB][hapmap]
rs7656001	0.82[CHB][hapmap]
rs7663699	0.85[CHB][hapmap]
rs7693233	0.85[CHB][hapmap]
rs7695098	0.88[CEU][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs919579	0.88[CEU][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs963207	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs9684316	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9991550	0.88[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470053	chr4:90879613-91439573	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv931074	chr4:90970476-91753697	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1007826	chr4:91049593-91438961	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv537177	chr4:91049593-91438961	Bivalent/Poised TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv999065	chr4:91049593-91520073	Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv879541	chr4:91156104-91253355	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv879542	chr4:91185206-91287204	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2870246	FAM190A	cis	cerebellum	SCAN
rs2870246	MXRA7	trans	lymphoblastoid	seeQTL
rs2870246	PTPRH	trans	brain	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:91222200-91244000	Weak transcription	Pancreas	Pancrea
2	chr4:91227200-91239000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:91228000-91234600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr4:91228200-91244000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr4:91228400-91245000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr4:91228600-91249600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:91229800-91238800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:91229800-91246200	Weak transcription	Fetal Intestine Large	intestine
9	chr4:91230800-91239200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:91231800-91249600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:91233200-91236200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr4:91233400-91244000	Weak transcription	Fetal Intestine Small	intestine
13	chr4:91233600-91235000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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