Variant report

Variant	rs10515939
Chromosome Location	chr2:179392785-179392786
allele	A/G
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	EP300	chr2:179392426-179393028	GM12878	blood:	n/a	n/a
2	BATF	chr2:179392498-179392872	GM12878	blood:	n/a	n/a
3	ATF2	chr2:179392255-179392901	GM12878	blood:	n/a	n/a
4	FOXM1	chr2:179392200-179392889	GM12878	blood:	n/a	n/a
5	BATF	chr2:179392222-179392892	GM12878	blood:	n/a	n/a
6	ATF2	chr2:179392303-179392821	GM12878	blood:	n/a	n/a
7	EBF1	chr2:179392700-179392819	GM12878	blood:	n/a	n/a
8	NFIC	chr2:179392156-179393036	GM12878	blood:	n/a	n/a
9	RUNX3	chr2:179392176-179392893	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179386919..179391089-chr2:179391647..179398872,11	K562	blood:

Variant related genes	Relation type
TTN-AS1	TF binding region
ENSG00000237298	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs16866378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16866380	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16866412	0.84[ASW][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];0.82[YRI][hapmap]
rs16866423	1.00[GIH][hapmap]
rs2115558	0.84[ASW][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];0.82[YRI][hapmap]
rs2278196	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2288324	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3731744	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3731752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813243	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3829749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62176135	0.86[EUR][1000 genomes]
rs72646841	0.96[ASN][1000 genomes]
rs72648270	0.95[EUR][1000 genomes];0.81[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	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv834468	chr2:179351116-179533625	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179388800-179393400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:179388800-179393400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:179388800-179395800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:179388800-179395800	Weak transcription	Placenta	Placenta
5	chr2:179388800-179395800	Weak transcription	Lung	lung
6	chr2:179388800-179396000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:179388800-179396200	Weak transcription	Fetal Kidney	kidney
8	chr2:179388800-179396200	Weak transcription	Gastric	stomach
9	chr2:179388800-179396200	Weak transcription	Pancreas	Pancrea
10	chr2:179388800-179403600	Weak transcription	Esophagus	oesophagus
11	chr2:179388800-179408000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:179388800-179408600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:179388800-179410600	Weak transcription	Colonic Mucosa	Colon
14	chr2:179388800-179411800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:179388800-179417600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:179388800-179429400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:179388800-179441800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:179388800-179448800	Weak transcription	Small Intestine	intestine
19	chr2:179388800-179495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr2:179389000-179395400	Weak transcription	Fetal Stomach	stomach
21	chr2:179389000-179395600	Weak transcription	Fetal Intestine Small	intestine
22	chr2:179389000-179395800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:179389000-179395800	Weak transcription	Aorta	Aorta
24	chr2:179389000-179396000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:179389000-179396000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:179389000-179396000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:179389000-179396200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:179389000-179396200	Weak transcription	Brain Substantia Nigra	brain
29	chr2:179389000-179396200	Weak transcription	Fetal Brain Female	brain
30	chr2:179389200-179395400	Weak transcription	Fetal Thymus	thymus
31	chr2:179389200-179396200	Weak transcription	Brain Anterior Caudate	brain
32	chr2:179389200-179396200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr2:179389200-179412600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr2:179389400-179394400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:179389400-179395200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:179389400-179395200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:179389400-179395600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:179389400-179395600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr2:179389400-179395600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr2:179389400-179395600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:179389400-179395600	Weak transcription	Right Atrium	heart
42	chr2:179389400-179395800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:179389400-179396000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr2:179389400-179396000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:179389400-179396000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:179389400-179396000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:179389400-179396000	Weak transcription	Brain Angular Gyrus	brain
48	chr2:179389400-179396000	Weak transcription	Fetal Lung	lung
49	chr2:179389400-179396000	Weak transcription	Ovary	ovary
50	chr2:179389400-179396000	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links