Variant report

Variant	rs2271496
Chromosome Location	chr3:113285276-113285277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:113277696..113281833-chr3:113284531..113288441,5	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10511325	1.00[GIH][hapmap]
rs11914782	1.00[MEX][hapmap]
rs11917149	0.87[EUR][1000 genomes]
rs11917288	0.87[EUR][1000 genomes]
rs11919031	1.00[MEX][hapmap]
rs11919330	0.87[EUR][1000 genomes]
rs11920725	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs11922598	0.88[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap]
rs11923128	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs11924109	0.87[EUR][1000 genomes]
rs11926687	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs11929418	1.00[MEX][hapmap]
rs1463639	0.87[EUR][1000 genomes]
rs1463641	1.00[MEX][hapmap]
rs1513288	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16845109	0.87[EUR][1000 genomes]
rs16860962	0.87[EUR][1000 genomes]
rs16861014	1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs16861023	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs16861025	0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs16861032	0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs16861045	1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs16861077	0.87[EUR][1000 genomes]
rs16861109	1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16861217	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17256551	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17256752	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17322613	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17325024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1906141	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs1989359	0.91[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2129431	0.87[EUR][1000 genomes]
rs2291412	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2306068	0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs2306070	0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs28472841	0.80[EUR][1000 genomes]
rs35758075	0.87[EUR][1000 genomes]
rs35812463	0.87[EUR][1000 genomes]
rs3732807	1.00[MEX][hapmap]
rs3732808	1.00[MEX][hapmap]
rs56685963	0.87[EUR][1000 genomes]
rs56772417	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57115529	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57164268	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58905600	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58988763	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59271111	0.87[EUR][1000 genomes]
rs59493419	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59673391	0.87[EUR][1000 genomes]
rs60940543	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61065093	0.87[EUR][1000 genomes]
rs61575357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6783691	1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs7636986	1.00[MEX][hapmap]
rs7650500	1.00[MEX][hapmap]
rs9863439	1.00[AFR][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	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv877349	chr3:113208224-113323787	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv877350	chr3:113208224-113332235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2271496	KCNMA1	trans	lymphoblastoid	seeQTL
rs2271496	CD200R1	cis	lymphoblastoid	seeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113276800-113294200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:113277600-113285600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr3:113279200-113300000	Weak transcription	Thymus	Thymus
4	chr3:113280000-113286400	Weak transcription	Fetal Thymus	thymus
5	chr3:113280200-113286400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:113280200-113299200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:113280200-113321600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:113280400-113304000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:113280600-113302400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:113280600-113314800	Weak transcription	Spleen	Spleen
11	chr3:113280800-113285600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr3:113281000-113285600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:113281000-113286000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr3:113281000-113286400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:113281000-113286400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:113281200-113286600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:113281400-113302200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:113281600-113286000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:113281600-113296400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:113281800-113296200	Strong transcription	Primary T cells from cord blood	blood
21	chr3:113283200-113289600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr3:113283200-113296200	Strong transcription	GM12878-XiMat	blood
23	chr3:113283400-113292200	Strong transcription	Primary B cells from cord blood	blood
24	chr3:113284800-113285800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:113284800-113286000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:113285000-113285800	Enhancers	HMEC	breast
27	chr3:113285000-113289800	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr3:113285000-113290600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr3:113285200-113285400	Enhancers	Esophagus	oesophagus
30	chr3:113285200-113285800	Enhancers	NHEK	skin
31	chr3:113285200-113287000	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr3:113285200-113290600	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr3:113285200-113329800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:113285200-113343400	Weak transcription	Small Intestine	intestine

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