Variant report

Variant	rs2475240
Chromosome Location	chr10:116284210-116284211
allele	A/G
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: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10749169	0.81[JPT][hapmap]
rs10749170	0.81[JPT][hapmap]
rs10885572	0.87[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10885573	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10885575	0.91[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11196779	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11196780	0.91[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11196781	0.90[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12569428	0.85[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2145893	0.90[ASN][1000 genomes]
rs2145894	0.83[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2247528	0.87[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2247624	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2475239	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs2475241	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2475242	0.87[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2483531	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2483571	0.87[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2483585	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2483587	0.87[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2483588	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2483595	0.85[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2483596	0.87[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2483599	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2483612	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2497708	0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs2497710	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497712	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2497717	0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2497718	0.87[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2497719	0.87[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2497720	0.82[AMR][1000 genomes]
rs2497721	0.83[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2497722	0.82[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes]
rs2497723	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35078486	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4144582	0.81[JPT][hapmap]
rs4514325	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4568918	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56001223	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56086836	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs867736	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs883511	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs883768	0.87[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9421179	0.86[CEU][hapmap];0.83[CHB][hapmap];0.89[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:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116243000-116286200	Weak transcription	Spleen	Spleen
2	chr10:116276600-116284600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr10:116277200-116284600	Weak transcription	Brain Angular Gyrus	brain
4	chr10:116277800-116284600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr10:116278200-116284600	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr10:116278800-116284600	Enhancers	Primary hematopoietic stem cells	blood
7	chr10:116278800-116284600	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr10:116278800-116285000	Genic enhancers	Left Ventricle	heart
9	chr10:116279400-116285800	Weak transcription	Psoas Muscle	Psoas
10	chr10:116279800-116284600	Weak transcription	Aorta	Aorta
11	chr10:116279800-116284800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr10:116279800-116286000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr10:116280000-116286200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr10:116280000-116286200	Weak transcription	Pancreas	Pancrea
15	chr10:116280200-116284600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr10:116280200-116284600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr10:116280200-116285000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr10:116280200-116285400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr10:116280200-116285800	Weak transcription	NHLF	lung
20	chr10:116280200-116286200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr10:116280400-116284600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr10:116280400-116284600	Weak transcription	HUVEC	blood vessel
23	chr10:116280400-116285000	Enhancers	A549	lung
24	chr10:116280800-116284400	Weak transcription	HMEC	breast
25	chr10:116280800-116285400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr10:116281000-116284800	Enhancers	Right Atrium	heart
27	chr10:116281200-116284800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr10:116281200-116285000	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr10:116281400-116284400	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr10:116281400-116284600	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr10:116281400-116285000	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr10:116281600-116284600	Enhancers	H1 Cell Line	embryonic stem cell
33	chr10:116281600-116285200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr10:116281800-116284600	Weak transcription	Fetal Intestine Large	intestine
35	chr10:116281800-116286200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr10:116282000-116284600	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr10:116282000-116285000	Weak transcription	Brain Anterior Caudate	brain
38	chr10:116282000-116286000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr10:116282000-116286000	Weak transcription	Brain Substantia Nigra	brain
40	chr10:116282000-116287000	Active TSS	Ovary	ovary
41	chr10:116282200-116284400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr10:116282200-116284800	Weak transcription	Fetal Intestine Small	intestine
43	chr10:116282200-116285600	Weak transcription	Brain Hippocampus Middle	brain
44	chr10:116282400-116284400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr10:116282400-116284600	Weak transcription	Adipose Nuclei	Adipose
46	chr10:116282400-116284800	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr10:116282400-116285200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr10:116282600-116284600	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr10:116282600-116284600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr10:116282600-116284600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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