Variant report

Variant	rs1433809
Chromosome Location	chr9:18817246-18817247
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10118205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1327505	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1583345	0.84[EUR][1000 genomes]
rs1583346	0.84[EUR][1000 genomes]
rs1965111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1980866	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6475253	0.85[AMR][1000 genomes]
rs7022488	0.84[EUR][1000 genomes]
rs7865744	0.83[CEU][hapmap];1.00[GIH][hapmap]
rs7871247	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised 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	9 gene(s)	inside rSNPs	diseases
2	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised 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	9 gene(s)	inside rSNPs	diseases
4	nsv1029449	chr9:18414752-18829127	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers 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 miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv540077	chr9:18414752-18829127	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv1030931	chr9:18414752-18903530	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised 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	6 gene(s)	inside rSNPs	diseases
7	nsv892692	chr9:18519699-19045502	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv949111	chr9:18758205-18994588	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1433809	PSIP1	cis	parietal	SCAN
rs1433809	HAUS6	cis	parietal	SCAN
rs1433809	PTPLAD2	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18788000-18825200	Weak transcription	HUVEC	blood vessel
2	chr9:18796800-18817400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:18800000-18824200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr9:18801200-18817600	Weak transcription	HSMMtube	muscle
5	chr9:18806400-18826000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:18806600-18824200	Weak transcription	Colon Smooth Muscle	Colon
7	chr9:18807000-18817600	Weak transcription	Fetal Muscle Leg	muscle
8	chr9:18807000-18824000	Weak transcription	Gastric	stomach
9	chr9:18810200-18817800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr9:18811600-18817600	Weak transcription	Aorta	Aorta
11	chr9:18813400-18817400	Weak transcription	Fetal Stomach	stomach
12	chr9:18814600-18824400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr9:18815200-18822200	Weak transcription	NHLF	lung
14	chr9:18815400-18829200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr9:18816200-18817400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:18817000-18818000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:18817000-18818400	Strong transcription	Fetal Heart	heart
18	chr9:18817000-18818400	Strong transcription	Fetal Muscle Trunk	muscle
19	chr9:18817000-18819200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:18817000-18819400	Strong transcription	NH-A	brain
21	chr9:18817000-18821400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr9:18817000-18823200	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr9:18817000-18823800	Strong transcription	Osteobl	bone
24	chr9:18817000-18824200	Strong transcription	NHDF-Ad	bronchial
25	chr9:18817000-18824400	Strong transcription	HSMM	muscle
26	chr9:18817200-18818000	Strong transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links