Variant report

Variant	rs9288006
Chromosome Location	chr2:152661831-152661832
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152639494..152642150-chr2:152659901..152662839,2	K562	blood:
2	chr2:152660681..152662473-chr2:152683493..152685563,2	K562	blood:
3	chr2:152661672..152663988-chr2:152664069..152666559,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162980	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10165921	0.91[JPT][hapmap]
rs10171724	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10180065	0.90[ASN][1000 genomes]
rs10184063	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10185966	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs10198530	0.91[ASN][1000 genomes]
rs10198531	0.93[ASN][1000 genomes]
rs10754989	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11682909	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11894672	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11896217	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12470190	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12472627	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs12693116	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1523181	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830418	1.00[CEU][hapmap]
rs1916301	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1916302	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2030588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2293221	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768658	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3922996	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3922997	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4233654	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4300824	0.82[GIH][hapmap];0.91[JPT][hapmap]
rs4306714	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4316939	0.91[JPT][hapmap]
rs4393745	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4414677	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.90[ASN][1000 genomes]
rs4450595	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4453694	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap]
rs4465763	0.81[CHB][hapmap]
rs4510224	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4552188	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4605370	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4664066	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4664498	0.84[GIH][hapmap];0.91[JPT][hapmap]
rs4664499	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap]
rs6433590	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6433680	1.00[CEU][hapmap]
rs6711382	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs6715027	0.90[ASN][1000 genomes]
rs6715607	0.82[ASN][1000 genomes]
rs6718439	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6740508	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6741567	1.00[CEU][hapmap]
rs6743968	1.00[CEU][hapmap]
rs6755393	1.00[CEU][hapmap]
rs7424335	0.84[GIH][hapmap];0.91[JPT][hapmap]
rs7557801	0.82[ASN][1000 genomes]
rs7564630	0.90[ASN][1000 genomes]
rs7580820	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7581532	0.86[ASN][1000 genomes]
rs7583060	0.90[ASN][1000 genomes]
rs7583148	0.90[ASN][1000 genomes]
rs7592798	0.96[ASN][1000 genomes]
rs9287998	0.86[EUR][1000 genomes];0.89[ASN][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	nsv934136	chr2:152308156-152664443	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv3693430	chr2:152648677-152681200	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152616800-152662400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:152617000-152669400	Weak transcription	Gastric	stomach
3	chr2:152619000-152677400	Weak transcription	Brain Substantia Nigra	brain
4	chr2:152623000-152680000	Weak transcription	Spleen	Spleen
5	chr2:152624000-152662600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr2:152631400-152667200	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:152632200-152679200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:152633000-152662200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:152634000-152665400	Weak transcription	Fetal Stomach	stomach
10	chr2:152634000-152683400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:152634800-152672200	Weak transcription	Right Ventricle	heart
12	chr2:152636000-152662400	Weak transcription	Fetal Brain Female	brain
13	chr2:152638600-152662000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:152638600-152665200	Weak transcription	Pancreas	Pancrea
15	chr2:152638600-152671000	Weak transcription	Thymus	Thymus
16	chr2:152638800-152665200	Weak transcription	Fetal Intestine Small	intestine
17	chr2:152638800-152668200	Weak transcription	Lung	lung
18	chr2:152638800-152672800	Weak transcription	Aorta	Aorta
19	chr2:152642000-152665400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:152642200-152662000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr2:152642200-152670400	Weak transcription	Brain Angular Gyrus	brain
22	chr2:152642800-152662600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr2:152643000-152668200	Weak transcription	NHDF-Ad	bronchial
24	chr2:152643400-152662200	Weak transcription	Brain Germinal Matrix	brain
25	chr2:152643400-152679000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:152644800-152662000	Weak transcription	Ovary	ovary
27	chr2:152644800-152676800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:152649000-152662400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:152649000-152680200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:152650200-152662600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:152654000-152662000	Weak transcription	Psoas Muscle	Psoas
32	chr2:152654200-152683400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:152654400-152678000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr2:152654400-152679000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:152655400-152671400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:152655400-152675200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr2:152655600-152664600	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr2:152655800-152662600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:152656200-152663400	Strong transcription	Liver	Liver
40	chr2:152656200-152664400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:152656400-152664200	Strong transcription	Primary B cells from peripheral blood	blood
42	chr2:152656400-152664600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:152656600-152671600	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr2:152656600-152672400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:152656800-152663400	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr2:152656800-152665200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:152656800-152665400	Strong transcription	HepG2	liver
48	chr2:152656800-152672400	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr2:152657000-152662400	Strong transcription	HUVEC	blood vessel
50	chr2:152657000-152664400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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