Variant report

Variant	rs13015283
Chromosome Location	chr2:190087467-190087468
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:190012942..190018195-chr2:190085147..190088368,4	MCF-7	breast:
2	chr2:190086028..190087990-chr2:190129145..190131338,2	MCF-7	breast:
3	chr2:190077868..190079394-chr2:190086183..190089052,2	MCF-7	breast:
4	chr2:190043908..190047710-chr2:190084994..190089422,4	MCF-7	breast:
5	chr2:190081246..190084128-chr2:190084434..190087476,3	K562	blood:
6	chr2:190085609..190089806-chr2:190139492..190143052,4	MCF-7	breast:
7	chr2:189957884..189960424-chr2:190085225..190088535,3	MCF-7	breast:
8	chr17:57922578..57924225-chr2:190085832..190088174,2	MCF-7	breast:
9	chr2:190010189..190015498-chr2:190084856..190090227,6	MCF-7	breast:
10	chr2:190086588..190088332-chr2:190150217..190152218,2	MCF-7	breast:
11	chr2:190087466..190090346-chr2:190148672..190151105,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228073	Chromatin interaction
ENSG00000204262	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10931400	0.90[EUR][1000 genomes]
rs10931404	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11681286	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11691604	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12104769	0.90[EUR][1000 genomes]
rs12105389	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12611950	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12615823	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12618438	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12621035	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12621806	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12621939	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12991770	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12993719	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12995956	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12999122	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12999996	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13004187	0.84[EUR][1000 genomes]
rs13004722	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13005652	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13005821	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13011374	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13011485	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13012327	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13012649	0.89[EUR][1000 genomes]
rs13016231	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13017413	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13019076	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13021508	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13022633	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13028967	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13029705	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13031211	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13031549	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13033421	0.90[EUR][1000 genomes]
rs1356162	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1356163	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1356164	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1356165	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1356167	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs1356168	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs1356977	0.81[EUR][1000 genomes]
rs1399991	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1399992	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1515874	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1515876	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1520857	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs1520859	0.84[EUR][1000 genomes]
rs1568334	0.91[EUR][1000 genomes]
rs1878085	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1949484	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1965422	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2138374	0.84[CEU][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2222256	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2351627	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2351633	0.92[AFR][1000 genomes]
rs2351636	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35475196	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35772309	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3914778	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4233801	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4428040	0.89[EUR][1000 genomes]
rs4666774	0.82[EUR][1000 genomes]
rs4667264	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4667265	0.92[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4667272	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4667274	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4667276	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4667277	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4998559	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60124911	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62182416	0.85[EUR][1000 genomes]
rs6434339	0.88[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6708419	0.92[CEU][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes]
rs6714088	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6719104	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6737071	0.91[EUR][1000 genomes]
rs7419888	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7561002	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7564611	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7576165	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7587147	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7587956	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7607133	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7609495	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190076000-190096800	Weak transcription	Aorta	Aorta
2	chr2:190078400-190087800	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:190084800-190088600	Enhancers	Hela-S3	cervix
4	chr2:190085800-190087600	Enhancers	HMEC	breast
5	chr2:190085800-190087600	Enhancers	NHEK	skin
6	chr2:190086000-190087600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:190086000-190087600	Enhancers	Fetal Intestine Large	intestine
8	chr2:190086000-190087600	Enhancers	Stomach Mucosa	stomach
9	chr2:190086000-190087600	Enhancers	NHDF-Ad	bronchial
10	chr2:190086000-190087800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:190086000-190088200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:190086200-190087600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:190086200-190087600	Enhancers	HSMM	muscle
14	chr2:190086200-190087800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:190086200-190087800	Enhancers	Osteobl	bone
16	chr2:190086200-190088200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:190086400-190087600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:190086400-190087600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:190086400-190087800	Enhancers	Rectal Smooth Muscle	rectum
20	chr2:190086600-190087600	Enhancers	Fetal Stomach	stomach
21	chr2:190086600-190087600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr2:190086800-190087600	Enhancers	Adipose Nuclei	Adipose
23	chr2:190086800-190087600	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr2:190086800-190087600	Enhancers	HSMMtube	muscle
25	chr2:190086800-190087600	Enhancers	NH-A	brain
26	chr2:190086800-190087800	Enhancers	NHLF	lung
27	chr2:190087000-190087800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:190087200-190087600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:190087200-190087600	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr2:190087200-190087600	Enhancers	Primary T cells from cord blood	blood
31	chr2:190087200-190087600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:190087200-190087600	Enhancers	Colonic Mucosa	Colon
33	chr2:190087200-190087600	Enhancers	Fetal Muscle Leg	muscle
34	chr2:190087200-190087600	Enhancers	Ovary	ovary
35	chr2:190087200-190087600	Enhancers	Pancreas	Pancrea
36	chr2:190087200-190087600	Enhancers	Psoas Muscle	Psoas
37	chr2:190087200-190087600	Enhancers	Right Atrium	heart
38	chr2:190087200-190087600	Flanking Active TSS	HUVEC	blood vessel
39	chr2:190087200-190088200	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr2:190087200-190088200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr2:190087200-190088200	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr2:190087200-190088200	Enhancers	Small Intestine	intestine
43	chr2:190087400-190087600	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr2:190087400-190087600	Flanking Active TSS	A549	lung
45	chr2:190087400-190088200	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr2:190087400-190088600	Enhancers	Muscle Satellite Cultured Cells	--
47	chr2:190087400-190090800	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links