Variant report

Variant	rs13003895
Chromosome Location	chr2:62982144-62982145
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10208675	0.85[ASN][1000 genomes]
rs11900596	0.85[ASN][1000 genomes]
rs13398408	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs181723	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2054835	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2539979	0.91[ASN][1000 genomes]
rs2553042	0.91[ASN][1000 genomes]
rs2710635	0.87[ASN][1000 genomes]
rs2901518	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2931488	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2969300	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34503992	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35801289	0.89[EUR][1000 genomes]
rs36009942	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs360786	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360787	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs360788	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs360789	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs360790	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs360793	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs360794	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs360795	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs360796	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs360798	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360802	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs360805	0.91[ASN][1000 genomes]
rs360806	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs36193012	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56065771	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6745862	0.81[ASN][1000 genomes]
rs6758263	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6760804	0.85[ASN][1000 genomes]
rs67657712	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7590973	0.85[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	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62953600-63001200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:62958200-62982800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr2:62958200-63010200	Weak transcription	Primary B cells from cord blood	blood
4	chr2:62961200-63011600	Weak transcription	NHLF	lung
5	chr2:62967000-62997000	Weak transcription	Dnd41	blood
6	chr2:62968400-62995200	Weak transcription	Left Ventricle	heart
7	chr2:62969800-62982800	Weak transcription	NHEK	skin
8	chr2:62969800-62987600	Weak transcription	HMEC	breast
9	chr2:62972200-62982200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:62972200-62983600	Weak transcription	Gastric	stomach
11	chr2:62972400-62987600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:62973000-62988800	Weak transcription	Adipose Nuclei	Adipose
13	chr2:62973400-62986800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:62973400-62987600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:62973800-62990800	Weak transcription	Fetal Lung	lung
16	chr2:62974200-63017200	Weak transcription	Primary T cells from cord blood	blood
17	chr2:62975200-62987600	Weak transcription	HSMM	muscle
18	chr2:62975200-62988800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:62975400-62985200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:62976000-62985600	Weak transcription	A549	lung
21	chr2:62976200-62983000	Weak transcription	HepG2	liver
22	chr2:62980200-62982600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr2:62980400-62983600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:62980800-62982200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:62980800-62982200	ZNF genes & repeats	Fetal Intestine Large	intestine
26	chr2:62980800-62982400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:62981000-62982200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:62981200-62982200	ZNF genes & repeats	Fetal Intestine Small	intestine
29	chr2:62981200-62982400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
30	chr2:62981200-62982400	ZNF genes & repeats	Fetal Muscle Leg	muscle
31	chr2:62981400-62982200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:62981400-62982200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
33	chr2:62981400-62982200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:62981400-62982200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:62981400-62982200	ZNF genes & repeats	Fetal Stomach	stomach
36	chr2:62981400-62982200	Strong transcription	Ovary	ovary
37	chr2:62981400-62982400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
38	chr2:62981400-62982400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:62981400-62982400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:62981400-62982400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
41	chr2:62981400-62982800	Strong transcription	Liver	Liver
42	chr2:62981600-62982400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:62981600-62982400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:62981600-62982400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
45	chr2:62981600-62982400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:62982000-62982200	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr2:62982000-62982800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:62982000-62983200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:62982000-62990800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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