Variant report

Variant	rs9394
Chromosome Location	chr12:32944546-32944547
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1046150	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10743802	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10743804	0.81[CHB][hapmap]
rs10771994	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10771995	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10772000	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772004	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs10844349	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11052243	0.80[ASN][1000 genomes]
rs11052246	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12612	0.82[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35960561	0.89[ASN][1000 genomes]
rs6488084	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6488086	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6488088	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6488089	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6488091	0.82[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6488092	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6488093	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7298089	0.89[ASN][1000 genomes]
rs7304383	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7308383	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7308500	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7312241	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7312621	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7956824	0.82[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7957460	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7968908	0.85[AMR][1000 genomes];0.93[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	esv1851844	chr12:32929596-32953032	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9394	SLC9A9	trans	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32933200-32944800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr12:32934200-32945200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:32936200-32948800	Weak transcription	Fetal Stomach	stomach
4	chr12:32936400-32947000	Weak transcription	Fetal Heart	heart
5	chr12:32937400-32945400	Weak transcription	NHEK	skin
6	chr12:32938600-32948600	Weak transcription	Gastric	stomach
7	chr12:32938600-32952200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:32938800-32945000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr12:32938800-32950600	Weak transcription	Brain Hippocampus Middle	brain
10	chr12:32939000-32944800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:32939200-32955200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:32939400-32945200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:32939600-32944800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:32939600-32945000	Weak transcription	Fetal Intestine Large	intestine
15	chr12:32940600-32946600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:32940800-32961800	Weak transcription	Colonic Mucosa	Colon
17	chr12:32941200-32949200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:32941800-32944800	Weak transcription	Placenta	Placenta
19	chr12:32941800-32945000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:32941800-32948800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr12:32941800-33033400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:32942000-32949400	Strong transcription	Liver	Liver
23	chr12:32942000-32957400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:32942200-32950600	Weak transcription	Ovary	ovary
25	chr12:32942400-32950600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:32942600-32944800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:32942600-32945000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:32943000-32945000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr12:32943200-32946000	Strong transcription	HMEC	breast
30	chr12:32943200-32948200	Weak transcription	Right Ventricle	heart
31	chr12:32943400-32945000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:32943400-32945000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr12:32943800-32947000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:32943800-32948600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr12:32943800-33026800	Weak transcription	Fetal Kidney	kidney
36	chr12:32944000-32949200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:32944200-32944600	Strong transcription	Fetal Intestine Small	intestine
38	chr12:32944200-32946000	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr12:32944200-32946000	Strong transcription	Left Ventricle	heart
40	chr12:32944200-32947400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr12:32944200-32948200	Weak transcription	Pancreas	Pancrea
42	chr12:32944200-32989400	Weak transcription	Hela-S3	cervix
43	chr12:32944400-32944600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr12:32944400-32945800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:32944400-32946000	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr12:32944400-32946200	Strong transcription	HepG2	liver
47	chr12:32944400-32949200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links