Variant report

Variant	rs17012680
Chromosome Location	chr2:33439467-33439468
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:33433433..33434972-chr2:33439448..33441761,2	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10048733	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10084248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10167324	0.94[ASN][1000 genomes]
rs10167399	0.94[ASN][1000 genomes]
rs10170980	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10173416	0.84[ASN][1000 genomes]
rs10189948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10195782	0.94[ASN][1000 genomes]
rs10201015	0.94[ASN][1000 genomes]
rs10201397	0.94[ASN][1000 genomes]
rs10201620	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10204479	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10205515	0.94[ASN][1000 genomes]
rs10514773	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11675702	0.84[ASN][1000 genomes]
rs11686962	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11691887	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11692723	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11886226	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11886337	0.94[ASN][1000 genomes]
rs11898777	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13392128	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13408945	0.94[ASN][1000 genomes]
rs13417478	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13417974	0.89[ASN][1000 genomes]
rs13431080	0.89[ASN][1000 genomes]
rs17012612	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17012615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17012621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17012646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17012655	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17012657	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17012674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17012691	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[ASN][1000 genomes]
rs17012720	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17012778	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2290427	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2290447	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3769546	1.00[JPT][hapmap]
rs4578839	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4641915	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs57095191	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs57119251	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs57408328	0.89[ASN][1000 genomes]
rs60523332	0.94[ASN][1000 genomes]
rs60912788	0.89[ASN][1000 genomes]
rs61609498	0.89[ASN][1000 genomes]
rs61754245	0.84[ASN][1000 genomes]
rs6543693	0.89[ASN][1000 genomes]
rs6543694	0.89[ASN][1000 genomes]
rs6543695	0.89[ASN][1000 genomes]
rs6543696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6543697	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6706122	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6718325	0.89[ASN][1000 genomes]
rs6722904	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6728561	0.94[ASN][1000 genomes]
rs6730109	0.89[ASN][1000 genomes]
rs6730341	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6734291	0.94[ASN][1000 genomes]
rs6746796	0.89[ASN][1000 genomes]
rs6752708	0.94[ASN][1000 genomes]
rs6757287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6757381	0.94[ASN][1000 genomes]
rs6760864	0.84[ASN][1000 genomes]
rs72855723	0.89[ASN][1000 genomes]
rs72855746	0.94[ASN][1000 genomes]
rs72855774	0.94[ASN][1000 genomes]
rs72855787	0.94[ASN][1000 genomes]
rs72858037	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs72858071	0.84[ASN][1000 genomes]
rs72858072	0.84[ASN][1000 genomes]
rs7583435	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7603774	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7606937	0.94[ASN][1000 genomes]
rs9308932	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs964701	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer 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	24 gene(s)	inside rSNPs	diseases
3	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	esv33628	chr2:33257484-33455355	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv873790	chr2:33369582-33466483	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33403800-33489800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:33409200-33441600	Weak transcription	Psoas Muscle	Psoas
3	chr2:33414600-33455400	Weak transcription	Fetal Stomach	stomach
4	chr2:33415200-33441600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:33415400-33441600	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:33423000-33439600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:33434200-33442200	Enhancers	HUVEC	blood vessel
8	chr2:33435800-33444400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:33436000-33441000	Enhancers	Stomach Smooth Muscle	stomach
10	chr2:33436200-33440000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:33436400-33439600	Enhancers	Aorta	Aorta
12	chr2:33436400-33439800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:33436400-33442200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:33436600-33440200	Weak transcription	HSMM	muscle
15	chr2:33436600-33441600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:33436600-33444200	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:33436800-33440200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:33436800-33440400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:33436800-33443800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:33436800-33455000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:33437200-33443400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:33437400-33444200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:33437600-33441200	Weak transcription	HSMMtube	muscle
24	chr2:33437600-33441600	Weak transcription	Liver	Liver
25	chr2:33437800-33439800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:33437800-33440000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:33437800-33442200	Enhancers	NH-A	brain
28	chr2:33437800-33444400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr2:33437800-33444600	Weak transcription	Hela-S3	cervix
30	chr2:33437800-33445200	Weak transcription	Fetal Kidney	kidney
31	chr2:33438000-33440000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:33438000-33443000	Enhancers	A549	lung
33	chr2:33438200-33439600	Weak transcription	K562	blood
34	chr2:33438200-33441600	Weak transcription	Esophagus	oesophagus
35	chr2:33438600-33440400	Enhancers	Rectal Smooth Muscle	rectum
36	chr2:33438800-33440000	Enhancers	Colon Smooth Muscle	Colon
37	chr2:33438800-33440600	Enhancers	NHLF	lung
38	chr2:33439000-33439600	Enhancers	Fetal Heart	heart
39	chr2:33439000-33439600	Weak transcription	NHDF-Ad	bronchial
40	chr2:33439000-33442000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:33439200-33440000	Enhancers	Stomach Mucosa	stomach
42	chr2:33439200-33440800	Enhancers	Right Atrium	heart
43	chr2:33439200-33442800	Enhancers	Left Ventricle	heart
44	chr2:33439400-33439600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr2:33439400-33439600	Enhancers	Gastric	stomach
46	chr2:33439400-33439600	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr2:33439400-33439600	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr2:33439400-33439600	Enhancers	NHEK	skin
49	chr2:33439400-33439800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr2:33439400-33439800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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