Variant report

Variant	rs4664066
Chromosome Location	chr2:152632406-152632407
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152631080..152635535-chr2:152637436..152642211,5	K562	blood:
2	chr2:152563836..152565601-chr2:152630541..152632941,2	K562	blood:
3	chr2:152630565..152634239-chr2:152680606..152685047,4	K562	blood:

Variant related genes	Relation type
ENSG00000162980	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10165921	0.85[JPT][hapmap]
rs10170273	0.82[GIH][hapmap]
rs10171724	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10180065	0.92[ASN][1000 genomes]
rs10184063	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10185966	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap]
rs10198530	0.93[ASN][1000 genomes]
rs10198531	0.95[ASN][1000 genomes]
rs10754989	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11680834	0.81[YRI][hapmap]
rs11682909	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11894672	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11896217	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12464543	0.83[CHB][hapmap]
rs12470190	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12472627	0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.99[ASN][1000 genomes]
rs12618063	0.84[GIH][hapmap]
rs12693116	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13005519	0.81[YRI][hapmap]
rs1523181	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16830418	1.00[CEU][hapmap]
rs1916301	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1916302	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2030588	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2293221	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768658	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3922996	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3922997	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4233654	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4300824	0.87[GIH][hapmap];0.85[JPT][hapmap]
rs4306714	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4316939	0.85[JPT][hapmap]
rs4393745	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4414677	0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[ASN][1000 genomes]
rs4450595	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4453694	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs4465763	0.86[CHB][hapmap]
rs4510224	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4552188	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4605370	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4664498	0.90[GIH][hapmap];0.85[JPT][hapmap]
rs4664499	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs6433590	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs6433656	0.81[YRI][hapmap]
rs6433680	1.00[CEU][hapmap];0.82[GIH][hapmap]
rs6711382	0.81[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap]
rs6712443	0.84[GIH][hapmap]
rs6712533	0.84[GIH][hapmap]
rs6715027	0.92[ASN][1000 genomes]
rs6715607	0.86[ASN][1000 genomes]
rs6716286	0.83[CHB][hapmap]
rs6718439	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6740508	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6741567	1.00[CEU][hapmap]
rs6743968	1.00[CEU][hapmap]
rs6755393	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs7424335	0.90[GIH][hapmap];0.95[JPT][hapmap]
rs7557801	0.85[ASN][1000 genomes]
rs7563441	0.83[CHB][hapmap]
rs7564024	0.80[GIH][hapmap]
rs7564630	0.92[ASN][1000 genomes]
rs7580820	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7581532	0.89[ASN][1000 genomes]
rs7583060	0.92[ASN][1000 genomes]
rs7583148	0.92[ASN][1000 genomes]
rs7592798	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9287998	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9288006	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]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152614600-152638000	Weak transcription	Pancreas	Pancrea
2	chr2:152616800-152644400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:152616800-152662400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:152617000-152632600	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:152617000-152638000	Weak transcription	Esophagus	oesophagus
6	chr2:152617000-152669400	Weak transcription	Gastric	stomach
7	chr2:152619000-152677400	Weak transcription	Brain Substantia Nigra	brain
8	chr2:152619800-152635800	Weak transcription	Fetal Brain Female	brain
9	chr2:152622000-152632800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr2:152622000-152632800	Weak transcription	Thymus	Thymus
11	chr2:152622200-152661800	Weak transcription	Fetal Kidney	kidney
12	chr2:152622600-152633000	Weak transcription	Right Ventricle	heart
13	chr2:152622600-152633800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:152623000-152680000	Weak transcription	Spleen	Spleen
15	chr2:152623200-152638000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:152623400-152632600	Weak transcription	Fetal Thymus	thymus
17	chr2:152623400-152635800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr2:152623400-152658800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr2:152623400-152659000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:152623600-152633800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:152623600-152659000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:152623800-152633600	Weak transcription	Fetal Intestine Small	intestine
23	chr2:152623800-152635800	Weak transcription	Brain Anterior Caudate	brain
24	chr2:152623800-152642000	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:152624000-152633400	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:152624000-152662600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:152624200-152633400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr2:152624200-152641400	Weak transcription	Brain Angular Gyrus	brain
29	chr2:152624200-152643000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr2:152624400-152635800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:152624400-152656800	Weak transcription	HepG2	liver
32	chr2:152625400-152660000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:152625600-152632600	Weak transcription	Ovary	ovary
34	chr2:152626800-152633600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:152626800-152643600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr2:152626800-152647000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:152627000-152638000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:152627200-152641800	Weak transcription	Brain Germinal Matrix	brain
39	chr2:152628000-152654800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr2:152628200-152641200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:152628800-152635600	Weak transcription	Adipose Nuclei	Adipose
42	chr2:152629000-152661800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr2:152629200-152633800	Weak transcription	Aorta	Aorta
44	chr2:152629200-152638000	Weak transcription	Fetal Lung	lung
45	chr2:152629200-152641600	Weak transcription	Psoas Muscle	Psoas
46	chr2:152630000-152641200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr2:152631200-152632600	Enhancers	K562	blood
48	chr2:152631200-152634000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:152631200-152636000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr2:152631200-152637000	Weak transcription	H1 Cell Line	embryonic stem cell

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