Variant report

Variant	rs7959230
Chromosome Location	chr12:32979318-32979319
allele	C/T
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	GATA3	chr12:32979254-32980278	SH-SY5Y	brain:	n/a	n/a
2	EP300	chr12:32979141-32980666	SK-N-SH	brain:	n/a	chr12:32980393-32980407

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:32978242..32979816-chr12:32981805..32984184,2	MCF-7	breast:

Variant related genes	Relation type
PKP2	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1046154	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10506100	1.00[CHB][hapmap]
rs10844370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052269	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11609744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615523	1.00[CHB][hapmap]
rs12311719	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12314796	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301619	1.00[CHB][hapmap]
rs7959085	1.00[ASN][1000 genomes]
rs7963225	1.00[CHB][hapmap]
rs7967264	1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[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	nsv530421	chr12:32825335-33465991	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1054440	chr12:32872999-33150460	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv532334	chr12:32884789-33034791	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv531961	chr12:32966192-32997952	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32941800-33033400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr12:32943800-33026800	Weak transcription	Fetal Kidney	kidney
3	chr12:32944200-32989400	Weak transcription	Hela-S3	cervix
4	chr12:32949200-32987000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:32949200-33007800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:32961000-32989800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:32963000-32986800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr12:32965000-32996200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:32971200-32981400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr12:32972000-33029000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:32973000-32989600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr12:32974000-32980800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr12:32974000-32987000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:32974200-33030400	Weak transcription	Right Ventricle	heart
15	chr12:32974400-32992600	Weak transcription	Pancreas	Pancrea
16	chr12:32974600-32981600	Weak transcription	Gastric	stomach
17	chr12:32974600-32987000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr12:32974600-32987000	Weak transcription	Colonic Mucosa	Colon
19	chr12:32974600-32991000	Weak transcription	Fetal Stomach	stomach
20	chr12:32974600-33004400	Weak transcription	Ovary	ovary
21	chr12:32975800-33020000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:32976000-32981000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:32976000-32983000	Weak transcription	Placenta	Placenta
24	chr12:32976000-32986600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:32976000-32986800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr12:32976200-32982800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr12:32976200-32987000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:32976400-32987000	Weak transcription	Liver	Liver
29	chr12:32977400-32982200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr12:32977400-32989600	Weak transcription	HMEC	breast
31	chr12:32977600-32979800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:32977600-32981000	Weak transcription	HepG2	liver
33	chr12:32977600-32981000	Weak transcription	NHEK	skin
34	chr12:32977600-32982800	Weak transcription	Fetal Intestine Large	intestine
35	chr12:32977600-32986600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr12:32977600-32986600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr12:32977600-32991000	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr12:32977800-32979600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:32977800-32980000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:32977800-32980800	Enhancers	Fetal Heart	heart
41	chr12:32977800-32982800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr12:32977800-32984000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr12:32978600-32980000	Enhancers	Placenta Amnion	Placenta Amnion
44	chr12:32979000-32979600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr12:32979000-32983400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:32979200-32980800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:32979200-32981000	Weak transcription	Left Ventricle	heart
48	chr12:32979200-32982000	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links