Variant report

Variant	rs1038570
Chromosome Location	chr2:62890171-62890172
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr2:62890133-62890372	HepG2	liver:	n/a	chr2:62890249-62890256 chr2:62890247-62890258 chr2:62890249-62890258
2	EP300	chr2:62889516-62892400	SK-N-SH	brain:	n/a	chr2:62889587-62889601 chr2:62890249-62890258 chr2:62891356-62891370 chr2:62891753-62891767 chr2:62889967-62889976
3	TCF12	chr2:62889568-62891548	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:62883737..62887558-chr2:62889986..62892467,3	K562	blood:

Variant related genes	Relation type
ENSG00000226622	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10208675	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.88[YRI][hapmap]
rs1038572	0.81[YRI][hapmap]
rs1038573	0.89[EUR][1000 genomes]
rs13398408	0.89[CHD][hapmap]
rs1386400	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1487074	0.82[YRI][hapmap]
rs1843778	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1872790	0.89[YRI][hapmap]
rs1997246	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2200562	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2421712	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2931488	1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2969300	1.00[JPT][hapmap]
rs34503992	0.89[CHD][hapmap]
rs36009942	0.89[CHD][hapmap]
rs360786	0.89[CHD][hapmap]
rs360793	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs360794	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs360795	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs360796	1.00[JPT][hapmap]
rs360798	0.89[CHD][hapmap]
rs360802	0.89[CHD][hapmap]
rs360805	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs360806	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs4273204	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671049	0.88[EUR][1000 genomes]
rs4671446	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6760804	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.88[YRI][hapmap]
rs7587936	0.81[EUR][1000 genomes]
rs9752159	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv834226	chr2:62745027-62894013	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv874232	chr2:62758044-62906084	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv834237	chr2:62762743-62926036	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62882000-62892000	Weak transcription	Fetal Intestine Large	intestine
2	chr2:62886400-62890600	Enhancers	NHLF	lung
3	chr2:62886400-62893400	Enhancers	HMEC	breast
4	chr2:62886600-62892800	Enhancers	Osteobl	bone
5	chr2:62886600-62894000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:62886600-62894200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:62886800-62892200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:62887200-62894000	Enhancers	HepG2	liver
9	chr2:62887400-62894000	Enhancers	Colon Smooth Muscle	Colon
10	chr2:62887400-62899000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:62887600-62892000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:62887600-62893600	Enhancers	Rectal Smooth Muscle	rectum
13	chr2:62888000-62890800	Weak transcription	Fetal Heart	heart
14	chr2:62888000-62891600	Enhancers	Fetal Kidney	kidney
15	chr2:62888000-62893800	Enhancers	Fetal Lung	lung
16	chr2:62888200-62891800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:62888600-62890200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:62888600-62890800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:62888600-62891800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr2:62888600-62892000	Weak transcription	Esophagus	oesophagus
21	chr2:62888600-62892400	Weak transcription	Pancreas	Pancrea
22	chr2:62888600-62893200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:62888600-62893200	Enhancers	NHEK	skin
24	chr2:62888800-62890200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:62888800-62890800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:62888800-62891000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr2:62888800-62891000	Enhancers	NHDF-Ad	bronchial
28	chr2:62888800-62891400	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr2:62888800-62891400	Weak transcription	Placenta	Placenta
30	chr2:62888800-62891800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:62888800-62892200	Enhancers	HSMM	muscle
32	chr2:62889000-62891000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:62889200-62891800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr2:62889200-62892200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:62889200-62892400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr2:62889400-62891600	Enhancers	Brain Hippocampus Middle	brain
37	chr2:62889400-62892200	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr2:62889400-62892200	Enhancers	HSMMtube	muscle
39	chr2:62889400-62893000	Enhancers	Adipose Nuclei	Adipose
40	chr2:62889600-62890400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:62889600-62890600	Enhancers	Fetal Muscle Leg	muscle
42	chr2:62889600-62891400	Enhancers	Stomach Smooth Muscle	stomach
43	chr2:62889600-62892200	Enhancers	Fetal Brain Male	brain
44	chr2:62889600-62892400	Enhancers	A549	lung
45	chr2:62889600-62894000	Enhancers	Fetal Stomach	stomach
46	chr2:62889800-62890600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:62889800-62890600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:62889800-62891000	Enhancers	Fetal Brain Female	brain
49	chr2:62889800-62891200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:62889800-62891800	Weak transcription	Lung	lung

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