Variant report

Variant	rs2475242
Chromosome Location	chr10:116285803-116285804
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:116275231..116277888-chr10:116283553..116286227,3	MCF-7	breast:
2	chr10:116260057..116262598-chr10:116283268..116286200,2	MCF-7	breast:
3	chr10:116277123..116279175-chr10:116283910..116286373,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229668	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10749169	0.81[JPT][hapmap]
rs10749170	0.81[JPT][hapmap]
rs10885572	0.92[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10885573	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10885575	0.95[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11196779	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11196780	0.95[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11196781	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12569428	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2145894	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2247528	0.92[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2247624	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2475239	0.89[CHB][hapmap]
rs2475240	0.87[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2475241	0.88[CEU][hapmap];0.89[CHB][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2483531	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2483564	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2483571	0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2483577	0.87[EUR][1000 genomes]
rs2483579	0.82[EUR][1000 genomes]
rs2483580	0.82[EUR][1000 genomes]
rs2483584	0.87[EUR][1000 genomes]
rs2483585	0.87[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2483587	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2483588	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2483595	0.91[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2483596	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2483599	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2483612	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2497708	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs2497710	0.92[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2497712	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2497717	0.84[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2497718	0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2497719	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2497720	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2497721	0.84[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2497722	0.86[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2497723	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35078486	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4144582	0.81[JPT][hapmap]
rs4514325	0.88[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4568918	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56001223	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56086836	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7094292	0.81[AMR][1000 genomes]
rs867736	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs883511	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs883768	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9421179	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116243000-116286200	Weak transcription	Spleen	Spleen
2	chr10:116279800-116286000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr10:116280000-116286200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr10:116280000-116286200	Weak transcription	Pancreas	Pancrea
5	chr10:116280200-116286200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr10:116281800-116286200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr10:116282000-116286000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr10:116282000-116286000	Weak transcription	Brain Substantia Nigra	brain
9	chr10:116282000-116287000	Active TSS	Ovary	ovary
10	chr10:116283200-116286000	Enhancers	Fetal Heart	heart
11	chr10:116283200-116286000	Weak transcription	Lung	lung
12	chr10:116283200-116286000	Enhancers	Small Intestine	intestine
13	chr10:116283200-116286200	Weak transcription	Placenta	Placenta
14	chr10:116283400-116286000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr10:116283600-116287400	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr10:116283800-116286000	Weak transcription	Right Ventricle	heart
17	chr10:116283800-116286800	Active TSS	Stomach Smooth Muscle	stomach
18	chr10:116284000-116286200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr10:116284000-116286800	Active TSS	Stomach Mucosa	stomach
20	chr10:116284600-116286200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr10:116284600-116286200	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr10:116284600-116286600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr10:116284600-116286800	Active TSS	Rectal Smooth Muscle	rectum
24	chr10:116284600-116287000	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr10:116284600-116287000	Flanking Active TSS	HUVEC	blood vessel
26	chr10:116284600-116287400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr10:116284800-116286200	Active TSS	Fetal Muscle Trunk	muscle
28	chr10:116284800-116286200	Active TSS	Right Atrium	heart
29	chr10:116284800-116286400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr10:116284800-116286800	Active TSS	Colonic Mucosa	Colon
31	chr10:116284800-116287000	Flanking Active TSS	Fetal Lung	lung
32	chr10:116284800-116287200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr10:116285000-116286000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr10:116285000-116286000	Weak transcription	Aorta	Aorta
35	chr10:116285000-116286000	Weak transcription	Left Ventricle	heart
36	chr10:116285000-116286000	Active TSS	GM12878-XiMat	blood
37	chr10:116285000-116286200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr10:116285000-116286200	Enhancers	Dnd41	blood
39	chr10:116285000-116286800	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr10:116285000-116286800	Active TSS	Primary T cells from cord blood	blood
41	chr10:116285000-116286800	Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr10:116285000-116287000	Active TSS	Fetal Stomach	stomach
43	chr10:116285000-116287200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr10:116285200-116286000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr10:116285200-116286000	Weak transcription	Esophagus	oesophagus
46	chr10:116285200-116286200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr10:116285200-116286200	Active TSS	Primary T cells fromperipheralblood	blood
48	chr10:116285200-116286200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr10:116285200-116286200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr10:116285200-116286200	Weak transcription	Brain Angular Gyrus	brain

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