Variant report

Variant	rs4414677
Chromosome Location	chr2:152624932-152624933
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152623599..152625917-chr2:152684439..152687152,2	K562	blood:
2	chr2:152624704..152626770-chr2:152632738..152634256,2	K562	blood:
3	chr2:152614524..152619932-chr2:152620577..152626819,11	K562	blood:
4	chr2:152623331..152625099-chr2:152684439..152686596,2	K562	blood:
5	chr2:152623919..152627757-chr2:152680404..152683778,4	K562	blood:
6	chr2:152623627..152626142-chr2:152629148..152631495,3	K562	blood:

Variant related genes	Relation type
ENSG00000162980	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10165921	1.00[CEU][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs10167462	0.81[GIH][hapmap]
rs10170273	0.90[GIH][hapmap]
rs10171724	0.87[ASN][1000 genomes]
rs10178880	0.87[GIH][hapmap]
rs10180065	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10184063	0.92[ASN][1000 genomes]
rs10185966	0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs10198530	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10198531	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10200512	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1054883	0.81[GIH][hapmap]
rs10754989	0.90[ASN][1000 genomes]
rs11676866	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11682909	0.90[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.92[ASN][1000 genomes]
rs11695661	0.81[GIH][hapmap]
rs11894672	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.89[ASN][1000 genomes]
rs11896217	0.87[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[ASN][1000 genomes]
rs12470190	0.90[ASN][1000 genomes]
rs12472627	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12618063	0.88[CEU][hapmap];0.92[GIH][hapmap]
rs12620077	0.87[GIH][hapmap]
rs12693116	0.99[ASN][1000 genomes]
rs13016166	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1523181	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.86[ASN][1000 genomes]
rs1799	0.81[GIH][hapmap]
rs1916301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1916302	0.92[ASN][1000 genomes]
rs2030588	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2293221	0.92[ASN][1000 genomes]
rs3768658	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.87[ASN][1000 genomes]
rs3922996	0.98[ASN][1000 genomes]
rs3922997	0.97[ASN][1000 genomes]
rs4233654	0.94[ASN][1000 genomes]
rs4266011	0.82[ASN][1000 genomes]
rs4300824	1.00[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs4306714	0.99[ASN][1000 genomes]
rs4316939	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs4393745	0.87[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[ASN][1000 genomes]
rs4413159	0.81[GIH][hapmap]
rs4450595	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4453694	0.82[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap]
rs4465763	0.81[CHB][hapmap]
rs4510224	0.87[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4536649	0.87[GIH][hapmap]
rs4552188	0.94[ASN][1000 genomes]
rs4605370	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4611637	0.81[GIH][hapmap]
rs4614931	0.83[GIH][hapmap]
rs4664066	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]
rs4664494	0.87[GIH][hapmap]
rs4664498	1.00[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs4664499	0.82[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.85[ASN][1000 genomes]
rs6433590	0.87[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs6711382	0.88[CEU][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap]
rs6711914	0.82[EUR][1000 genomes]
rs6712443	0.87[CEU][hapmap];0.92[GIH][hapmap]
rs6712533	0.88[CEU][hapmap];0.92[GIH][hapmap]
rs6713162	0.85[GIH][hapmap]
rs6715027	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6715607	0.92[ASN][1000 genomes]
rs6716286	0.81[GIH][hapmap]
rs6718439	0.92[ASN][1000 genomes]
rs6734148	0.81[GIH][hapmap]
rs6740508	0.99[ASN][1000 genomes]
rs6741567	0.85[ASN][1000 genomes]
rs6744121	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6749823	0.83[ASN][1000 genomes]
rs6755393	0.89[MEX][hapmap]
rs7424335	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs7426114	0.87[GIH][hapmap]
rs7557801	0.92[ASN][1000 genomes]
rs7564024	0.87[GIH][hapmap]
rs7564630	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580820	0.89[ASN][1000 genomes]
rs7581532	0.96[ASN][1000 genomes]
rs7583060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7592798	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7596744	0.81[GIH][hapmap]
rs9287990	0.85[GIH][hapmap]
rs9287998	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9288006	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]

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:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152611000-152632400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:152614600-152638000	Weak transcription	Pancreas	Pancrea
3	chr2:152616800-152644400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:152616800-152662400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:152617000-152632600	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:152617000-152638000	Weak transcription	Esophagus	oesophagus
7	chr2:152617000-152669400	Weak transcription	Gastric	stomach
8	chr2:152618200-152631200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:152618400-152625200	Strong transcription	Aorta	Aorta
10	chr2:152619000-152677400	Weak transcription	Brain Substantia Nigra	brain
11	chr2:152619800-152635800	Weak transcription	Fetal Brain Female	brain
12	chr2:152620200-152632000	Enhancers	Primary B cells from cord blood	blood
13	chr2:152621600-152627800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:152622000-152632800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr2:152622000-152632800	Weak transcription	Thymus	Thymus
16	chr2:152622200-152625200	Enhancers	Psoas Muscle	Psoas
17	chr2:152622200-152632200	Weak transcription	Fetal Intestine Large	intestine
18	chr2:152622200-152661800	Weak transcription	Fetal Kidney	kidney
19	chr2:152622600-152633000	Weak transcription	Right Ventricle	heart
20	chr2:152622600-152633800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:152622800-152625200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr2:152622800-152629600	Enhancers	Primary B cells from peripheral blood	blood
23	chr2:152623000-152680000	Weak transcription	Spleen	Spleen
24	chr2:152623200-152638000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:152623400-152626200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:152623400-152631800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr2:152623400-152632400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:152623400-152632600	Weak transcription	Fetal Thymus	thymus
29	chr2:152623400-152635800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:152623400-152658800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:152623400-152659000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:152623600-152633800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:152623600-152659000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:152623800-152628400	Weak transcription	Primary T cells from cord blood	blood
35	chr2:152623800-152631600	Weak transcription	Lung	lung
36	chr2:152623800-152633600	Weak transcription	Fetal Intestine Small	intestine
37	chr2:152623800-152635800	Weak transcription	Brain Anterior Caudate	brain
38	chr2:152623800-152642000	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr2:152624000-152626200	Weak transcription	Fetal Stomach	stomach
40	chr2:152624000-152627800	Weak transcription	NHLF	lung
41	chr2:152624000-152628000	Weak transcription	Placenta	Placenta
42	chr2:152624000-152628600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:152624000-152633400	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr2:152624000-152662600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:152624200-152625000	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr2:152624200-152625200	Enhancers	K562	blood
47	chr2:152624200-152626200	Weak transcription	Fetal Muscle Leg	muscle
48	chr2:152624200-152626600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:152624200-152626600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:152624200-152627400	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links