Variant report

Variant	rs10209615
Chromosome Location	chr2:231089943-231089944
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:231089909-231091478	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:231089884-231091284	GM12891	blood:	n/a	n/a
3	POLR2A	chr2:231089800-231091367	GM12892	blood:	n/a	n/a
4	POLR2A	chr2:231089755-231091410	GM12892	blood:	n/a	n/a
5	POLR2A	chr2:231089903-231091281	Raji	blood:	n/a	n/a
6	RELA	chr2:231089827-231091287	GM15510	blood:	n/a	n/a
7	NFIC	chr2:231089779-231091691	GM12878	blood:	n/a	n/a
8	MXI1	chr2:231089718-231091387	GM12878	blood:	n/a	n/a
9	MTA3	chr2:231089614-231091438	GM12878	blood:	n/a	n/a
10	STAT1	chr2:231089893-231090826	GM12878	blood:	n/a	n/a
11	PML	chr2:231089728-231091436	GM12878	blood:	n/a	chr2:231091236-231091244

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:231082900..231084679-chr2:231088128..231090414,2	K562	blood:

Variant related genes	Relation type
SP140	TF binding region
ENSG00000135899	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10198539	0.93[CEU][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10201872	1.00[ASW][hapmap];0.94[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10202244	1.00[ASW][hapmap];0.94[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10498246	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs13384787	0.89[ASW][hapmap];0.94[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13385151	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13397985	0.83[CEU][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13426106	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1946410	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28445040	0.83[CEU][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28693552	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34855578	0.85[EUR][1000 genomes]
rs35008063	0.88[EUR][1000 genomes]
rs35857956	0.85[EUR][1000 genomes]
rs6436922	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6705808	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6716753	0.84[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6738805	0.81[CEU][hapmap];0.86[AFR][1000 genomes]
rs6743984	0.84[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs7423615	0.83[CEU][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7557418	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7563433	0.83[CEU][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7584894	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9989735	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9989746	0.89[ASW][hapmap];0.94[CEU][hapmap];0.90[GIH][hapmap];0.88[LWK][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9989835	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs9989899	0.83[CEU][hapmap];0.89[TSI][hapmap];0.85[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	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv869834	chr2:231045013-231139827	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv998291	chr2:231045388-231136278	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv584666	chr2:231050715-231106621	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10209615	SP140	Cis_1M	lymphoblastoid	RTeQTL
rs10209615	SP140	cis	lymphoblastoid	seeQTL
rs10209615	TRIP12	cis	parietal	SCAN
rs10209615	SP110	Cis_1M	lymphoblastoid	RTeQTL
rs10209615	ALPI	cis	cerebellum	SCAN
rs10209615	SP110	cis	lymphoblastoid	seeQTL
rs10209615	SP140	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231085000-231094800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:231085400-231090000	Weak transcription	Esophagus	oesophagus
3	chr2:231085400-231090600	Weak transcription	Small Intestine	intestine
4	chr2:231085400-231092000	Weak transcription	Pancreas	Pancrea
5	chr2:231085600-231090200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:231086400-231090400	Weak transcription	Fetal Thymus	thymus
7	chr2:231086400-231095000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:231088200-231090000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr2:231088400-231090000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr2:231088400-231090000	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr2:231088400-231090400	Flanking Active TSS	GM12878-XiMat	blood
12	chr2:231088400-231091000	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr2:231088800-231091200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr2:231088800-231091800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:231089000-231090000	Weak transcription	Spleen	Spleen
16	chr2:231089200-231091200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr2:231089400-231090400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr2:231089600-231090200	Flanking Active TSS	Primary B cells from peripheral blood	blood
19	chr2:231089600-231090200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr2:231089800-231090000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:231089800-231090200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:231089800-231090200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr2:231089800-231090200	Enhancers	Duodenum Mucosa	Duodenum
24	chr2:231089800-231090400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
25	chr2:231089800-231090400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:231089800-231090400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr2:231089800-231090400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:231089800-231090600	Enhancers	Primary hematopoietic stem cells	blood
29	chr2:231089800-231090800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:231089800-231091000	Active TSS	Rectal Smooth Muscle	rectum
31	chr2:231089800-231091400	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr2:231089800-231092200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:231089800-231093200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links