Variant report

Variant	rs4963644
Chromosome Location	chr12:26139403-26139404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:26110616..26112920-chr12:26135351..26139719,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246695	Chromatin interaction
ENSG00000123094	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10505989	0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs10842654	0.87[CEU][hapmap]
rs12425863	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12426668	0.88[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes]
rs1495649	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1533244	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16929681	0.84[CHB][hapmap]
rs16929780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16929815	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16929857	0.84[AMR][1000 genomes]
rs16929860	0.87[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16929894	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16929895	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16929904	1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16929970	0.92[JPT][hapmap];0.81[AMR][1000 genomes]
rs16929998	0.87[CEU][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes]
rs2137550	0.92[JPT][hapmap]
rs2343200	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2669565	0.92[JPT][hapmap]
rs2669566	0.92[JPT][hapmap]
rs2669568	0.83[JPT][hapmap]
rs2729626	0.92[JPT][hapmap]
rs2729638	0.82[JPT][hapmap]
rs2729643	0.83[JPT][hapmap]
rs2729644	0.84[JPT][hapmap]
rs2729649	0.84[JPT][hapmap]
rs3803008	0.84[AMR][1000 genomes]
rs4963643	0.91[AMR][1000 genomes]
rs4963947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4963952	0.92[JPT][hapmap]
rs57082706	0.81[AMR][1000 genomes]
rs57791860	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61123975	0.81[AMR][1000 genomes]
rs6487526	0.83[JPT][hapmap]
rs73074872	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73074898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73077103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73077131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73077152	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73077161	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73077176	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73077179	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73079010	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73079023	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73079024	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73079069	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73080925	0.81[AMR][1000 genomes]
rs7961722	0.92[JPT][hapmap]
rs9804876	0.87[CEU][hapmap];0.83[AMR][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	esv2758300	chr12:25992331-26161116	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	esv2759886	chr12:25992331-26161116	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv898931	chr12:26123345-26192936	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv522351	chr12:26127230-26149703	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26117600-26150000	Weak transcription	Hela-S3	cervix
2	chr12:26129800-26143000	Enhancers	Colon Smooth Muscle	Colon
3	chr12:26131000-26145400	Weak transcription	Lung	lung
4	chr12:26131000-26146000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr12:26131000-26146200	Weak transcription	HSMM	muscle
6	chr12:26132400-26141600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:26132400-26146800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:26133000-26144600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:26133000-26144600	Weak transcription	HMEC	breast
10	chr12:26133000-26144600	Weak transcription	NHEK	skin
11	chr12:26133000-26145200	Weak transcription	NH-A	brain
12	chr12:26133000-26145200	Weak transcription	Osteobl	bone
13	chr12:26134200-26148000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:26134400-26141600	Weak transcription	NHDF-Ad	bronchial
15	chr12:26134400-26145400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:26134400-26145400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:26134400-26147800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:26136000-26141400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:26136400-26139800	Enhancers	Rectal Smooth Muscle	rectum
20	chr12:26136800-26142000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr12:26137200-26140200	Enhancers	Ovary	ovary
22	chr12:26137200-26140200	Enhancers	Psoas Muscle	Psoas
23	chr12:26137200-26143200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:26137400-26139800	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr12:26137600-26139600	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr12:26137600-26139800	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr12:26137800-26139600	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr12:26137800-26139600	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr12:26137800-26139800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr12:26137800-26139800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:26138000-26139600	Enhancers	Brain Substantia Nigra	brain
32	chr12:26138000-26139800	Enhancers	H9 Cell Line	embryonic stem cell
33	chr12:26138000-26139800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:26138000-26139800	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr12:26138000-26140400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:26138000-26140400	Enhancers	Fetal Intestine Large	intestine
37	chr12:26138000-26140400	Enhancers	Fetal Intestine Small	intestine
38	chr12:26138200-26139600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:26138200-26139600	Enhancers	Left Ventricle	heart
40	chr12:26138200-26140400	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr12:26138400-26141200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:26138400-26141200	Weak transcription	Fetal Lung	lung
43	chr12:26138400-26146800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:26138600-26139600	Enhancers	Pancreas	Pancrea
45	chr12:26138600-26140000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:26138800-26140400	Enhancers	Fetal Heart	heart
47	chr12:26138800-26141200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr12:26138800-26141400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr12:26138800-26141600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr12:26138800-26145400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links