Variant report

Variant	rs10962493
Chromosome Location	chr9:16572137-16572138
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:34853813..34854390-chr9:16572137..16572637,2	MCF-7	breast:

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10116857	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10117448	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10120281	0.88[EUR][1000 genomes]
rs10121959	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123480	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs10123558	0.82[CEU][hapmap]
rs10511622	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10733312	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10738437	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs10738439	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10756763	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs10810576	0.82[CEU][hapmap]
rs10962488	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10962492	0.82[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10962494	0.82[CEU][hapmap]
rs10962511	1.00[CEU][hapmap]
rs12000225	0.86[ASN][1000 genomes]
rs12000228	0.86[ASN][1000 genomes]
rs12000426	0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12002297	0.86[ASN][1000 genomes]
rs12002673	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12004947	1.00[ASN][1000 genomes]
rs12335443	1.00[JPT][hapmap]
rs12337676	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12338548	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12340504	0.82[EUR][1000 genomes]
rs12343239	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12343306	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12350242	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12350853	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12352543	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1337393	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1337400	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1415473	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1415474	1.00[CEU][hapmap]
rs1415475	0.86[EUR][1000 genomes]
rs1415476	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs16934806	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs16934842	0.88[EUR][1000 genomes]
rs16934855	0.80[EUR][1000 genomes]
rs1807023	0.92[AMR][1000 genomes]
rs1927616	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1927617	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927618	0.82[CEU][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs1927626	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1952345	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1952346	1.00[CEU][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2065937	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2095657	0.80[EUR][1000 genomes]
rs2382808	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2382809	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2382810	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28414647	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28483319	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28490464	0.88[EUR][1000 genomes]
rs28593297	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28602416	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28714603	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28733737	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2891072	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56170891	0.82[AMR][1000 genomes]
rs6475059	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6475060	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6475062	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6475063	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7018594	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7021199	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7022813	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7029578	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7029648	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7030387	0.88[AMR][1000 genomes]
rs7035791	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7048399	0.82[EUR][1000 genomes]
rs7049082	0.82[AMR][1000 genomes]
rs725011	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs73417483	0.86[ASN][1000 genomes]
rs73419403	0.86[ASN][1000 genomes]
rs7350234	1.00[CEU][hapmap]
rs7470623	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7847768	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7850123	0.82[CEU][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7856477	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs7857751	0.86[ASN][1000 genomes]
rs7858025	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7859971	0.86[EUR][1000 genomes]
rs7861969	0.86[ASN][1000 genomes]
rs7863885	0.82[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870380	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7872747	0.82[AMR][1000 genomes]
rs7872838	0.82[AMR][1000 genomes]
rs7873338	0.80[EUR][1000 genomes]
rs943744	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs943745	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs943748	1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv528443	chr9:16570142-16581967	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16553000-16575200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:16556400-16575600	Weak transcription	HSMM	muscle
3	chr9:16566600-16573000	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr9:16568800-16575200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:16569600-16572200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr9:16569600-16572400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr9:16569600-16572400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr9:16569800-16572400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr9:16569800-16582400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:16570000-16572200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:16570400-16572400	Enhancers	Colon Smooth Muscle	Colon
12	chr9:16570600-16572200	Enhancers	Primary hematopoietic stem cells	blood
13	chr9:16570600-16572200	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr9:16570600-16572600	Enhancers	Osteobl	bone
15	chr9:16570600-16572800	Enhancers	NHLF	lung
16	chr9:16570600-16573000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:16570800-16572800	Enhancers	NHDF-Ad	bronchial
18	chr9:16570800-16575800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr9:16571000-16572400	Enhancers	Adipose Nuclei	Adipose
20	chr9:16571000-16572800	Enhancers	Fetal Lung	lung
21	chr9:16571000-16573600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:16571200-16572800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:16571200-16572800	Enhancers	Fetal Kidney	kidney
24	chr9:16571200-16573200	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr9:16571200-16575200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:16571400-16572400	Flanking Active TSS	A549	lung
27	chr9:16571400-16572800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:16571400-16572800	Enhancers	Fetal Thymus	thymus
29	chr9:16571400-16582000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr9:16571600-16572200	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr9:16571600-16572200	Enhancers	Stomach Smooth Muscle	stomach
32	chr9:16571600-16572400	Enhancers	Fetal Stomach	stomach
33	chr9:16571600-16572400	Weak transcription	Ovary	ovary
34	chr9:16571600-16573000	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr9:16571600-16573200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:16571800-16572200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:16571800-16572400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr9:16571800-16572400	Weak transcription	Colonic Mucosa	Colon
39	chr9:16571800-16572400	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr9:16571800-16572600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr9:16571800-16574800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr9:16571800-16575600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr9:16572000-16572400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr9:16572000-16572600	Flanking Active TSS	Liver	Liver
45	chr9:16572000-16573000	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr9:16572000-16575400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr9:16572000-16581800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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