Variant report

Variant	rs13261887
Chromosome Location	chr8:19461590-19461591
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10088454	0.84[GIH][hapmap]
rs10089231	0.84[GIH][hapmap]
rs10100557	1.00[CEU][hapmap]
rs10100589	0.87[GIH][hapmap]
rs10105363	0.84[GIH][hapmap]
rs10106622	0.87[GIH][hapmap]
rs10109274	0.84[GIH][hapmap]
rs1105046	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11993402	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs13248137	1.00[CEU][hapmap]
rs13250084	0.88[EUR][1000 genomes]
rs13252416	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13260856	0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13263246	0.87[GIH][hapmap]
rs13281882	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs13282951	0.84[GIH][hapmap]
rs17128604	0.84[GIH][hapmap]
rs17128707	1.00[CEU][hapmap]
rs17480419	1.00[CEU][hapmap]
rs28418918	0.84[EUR][1000 genomes]
rs28558562	0.87[ASN][1000 genomes]
rs28690902	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34267078	0.84[EUR][1000 genomes]
rs34453606	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35101845	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4457347	0.81[ASN][1000 genomes]
rs4472533	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs4565470	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4574860	0.97[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4636223	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4922066	0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs59244617	0.84[EUR][1000 genomes]
rs6980558	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs6984585	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6988797	0.93[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6988825	0.80[CHD][hapmap];0.93[JPT][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6992213	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs6993026	1.00[CEU][hapmap];0.90[GIH][hapmap]
rs6995903	0.87[GIH][hapmap]
rs6996593	1.00[CEU][hapmap]
rs6996750	1.00[CEU][hapmap]
rs6997538	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7003381	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7840615	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv948861	chr8:19199688-19609029	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv949304	chr8:19199688-19625912	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer 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
4	esv34007	chr8:19252602-19482098	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv890625	chr8:19368697-19799641	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv890626	chr8:19383697-19483259	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv890627	chr8:19389865-19561997	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv610754	chr8:19419494-19525294	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1021575	chr8:19430653-19623452	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv610756	chr8:19434021-19471977	Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1025271	chr8:19435147-19574969	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13261887	BCR	trans	lymphoblastoid	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19445600-19481400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr8:19456200-19479600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr8:19457600-19465000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr8:19457600-19472200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr8:19459400-19472000	Weak transcription	Primary T cells from cord blood	blood
6	chr8:19459400-19472200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr8:19459800-19463200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr8:19460200-19462200	Weak transcription	Primary B cells from cord blood	blood
9	chr8:19460200-19462400	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr8:19460200-19462400	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr8:19460200-19462600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr8:19460200-19462800	Weak transcription	Ovary	ovary
13	chr8:19460200-19463000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr8:19460200-19463000	Weak transcription	Placenta	Placenta
15	chr8:19460200-19463400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr8:19460200-19465000	Weak transcription	Adipose Nuclei	Adipose
17	chr8:19460200-19467400	Weak transcription	Spleen	Spleen
18	chr8:19460200-19474200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr8:19460200-19474200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr8:19460400-19461800	Enhancers	Right Atrium	heart
21	chr8:19460400-19461800	Enhancers	A549	lung
22	chr8:19460400-19463000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr8:19460400-19463200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr8:19460400-19463200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr8:19460400-19464600	Weak transcription	Right Ventricle	heart
26	chr8:19460400-19464800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr8:19460400-19464800	Weak transcription	Brain Hippocampus Middle	brain
28	chr8:19460400-19465000	Weak transcription	Aorta	Aorta
29	chr8:19460400-19465000	Weak transcription	NHLF	lung
30	chr8:19460400-19465600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr8:19460400-19466200	Weak transcription	Brain Angular Gyrus	brain
32	chr8:19460400-19466600	Enhancers	Fetal Lung	lung
33	chr8:19460800-19461600	Strong transcription	Hela-S3	cervix
34	chr8:19461000-19461800	Weak transcription	Fetal Brain Male	brain
35	chr8:19461000-19462800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr8:19461000-19465000	Weak transcription	Brain Germinal Matrix	brain
37	chr8:19461000-19465000	Weak transcription	Esophagus	oesophagus
38	chr8:19461000-19465000	Weak transcription	Left Ventricle	heart
39	chr8:19461200-19464400	Weak transcription	Fetal Muscle Leg	muscle
40	chr8:19461400-19462000	Enhancers	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links