Variant report

Variant	rs11681966
Chromosome Location	chr2:100759457-100759458
allele	A/C
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	FOXM1	chr2:100758755-100759528	GM12878	blood:	n/a	n/a
2	IRF4	chr2:100758773-100759471	GM12878	blood:	n/a	n/a
3	EP300	chr2:100758905-100759536	GM12878	blood:	n/a	chr2:100759110-100759124
4	SPI1	chr2:100758535-100759678	GM12878	blood:	n/a	chr2:100759648-100759661
5	MTA3	chr2:100758120-100759703	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:100756765-100759686	Raji	blood:	n/a	n/a
7	RELA	chr2:100758788-100759603	GM18505	blood:	n/a	n/a
8	STAT5A	chr2:100758432-100759817	GM12878	blood:	n/a	chr2:100759445-100759456 chr2:100758535-100758546 chr2:100759632-100759639 chr2:100759420-100759431

Variant related genes	Relation type
AFF3	TF binding region

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

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10185059	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10185510	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10197987	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10496344	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11123809	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11123810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123811	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11123812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123813	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11679078	0.82[ASN][1000 genomes]
rs11681227	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11682173	0.81[ASN][1000 genomes]
rs11690905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891046	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11899489	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11900482	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902705	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12712064	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12712065	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12712067	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12712068	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712071	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12987209	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12987212	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13003982	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13005282	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13019618	0.82[ASN][1000 genomes]
rs13032454	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13415465	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13415583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1370353	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1821826	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1821827	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2009094	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2009095	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2118280	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2164712	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2309752	0.96[ASN][1000 genomes]
rs4490209	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4850920	0.82[ASN][1000 genomes]
rs4850921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4851252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4851253	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851254	0.81[ASN][1000 genomes]
rs4851256	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4851257	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56054309	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7590378	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7593261	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7608424	0.92[ASN][1000 genomes]

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	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv582530	chr2:100739970-100774287	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv527481	chr2:100753490-100763006	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11681966	AFF3	cis	parietal	SCAN
rs11681966	MGAT4A	cis	parietal	SCAN
rs11681966	MRPL30	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100746200-100764800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:100753800-100759800	Flanking Active TSS	Dnd41	blood
3	chr2:100756800-100759800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:100757400-100759600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:100758200-100761600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr2:100758400-100759600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:100758400-100759600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr2:100758800-100765600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:100759000-100759600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:100759000-100759800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr2:100759000-100763000	Weak transcription	Adipose Nuclei	Adipose
12	chr2:100759200-100759600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr2:100759200-100759800	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr2:100759200-100759800	Enhancers	Primary T cells fromperipheralblood	blood
15	chr2:100759200-100760400	Enhancers	Fetal Thymus	thymus
16	chr2:100759200-100760600	Enhancers	Primary hematopoietic stem cells	blood
17	chr2:100759200-100760800	ZNF genes & repeats	GM12878-XiMat	blood
18	chr2:100759200-100761400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:100759200-100763400	Enhancers	Primary B cells from peripheral blood	blood
20	chr2:100759400-100759600	Enhancers	Primary T cells from cord blood	blood
21	chr2:100759400-100759600	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr2:100759400-100759600	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr2:100759400-100759800	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr2:100759400-100759800	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr2:100759400-100759800	Enhancers	Spleen	Spleen
26	chr2:100759400-100760000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr2:100759400-100760000	Enhancers	Thymus	Thymus
28	chr2:100759400-100760200	Enhancers	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links