Variant report

Variant	rs7874819
Chromosome Location	chr9:101809368-101809369
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11788317	0.84[ASN][1000 genomes]
rs11789439	0.88[CEU][hapmap];0.82[MEX][hapmap]
rs12683611	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16918167	0.82[CEU][hapmap];0.81[CHB][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3780617	0.88[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3780620	0.88[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743311	0.84[AFR][1000 genomes]
rs4743312	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743313	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743314	0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7030799	0.88[CEU][hapmap]
rs7031588	0.83[CEU][hapmap];0.86[MEX][hapmap]
rs7038068	0.87[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs7047475	0.88[CEU][hapmap]
rs7855612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869776	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs976241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv466442	chr9:101788522-101816399	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv614954	chr9:101788522-101816399	Strong transcription Genic enhancers Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv893618	chr9:101800106-101886071	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7874819	TSTD2	cis	parietal	SCAN
rs7874819	C9orf30	cis	parietal	SCAN
rs7874819	COL15A1	cis	lymphoblastoid	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101761600-101814400	Weak transcription	Gastric	stomach
2	chr9:101782000-101819800	Weak transcription	Colonic Mucosa	Colon
3	chr9:101789000-101812000	Weak transcription	Esophagus	oesophagus
4	chr9:101793800-101837600	Weak transcription	Psoas Muscle	Psoas
5	chr9:101798200-101811400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr9:101798400-101819800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr9:101799200-101814600	Weak transcription	Pancreas	Pancrea
8	chr9:101804000-101809600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:101804000-101820000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:101804200-101809400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr9:101805800-101810000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:101805800-101819400	Strong transcription	Adipose Nuclei	Adipose
13	chr9:101805800-101820600	Weak transcription	Right Ventricle	heart
14	chr9:101806400-101810600	Strong transcription	Ovary	ovary
15	chr9:101806600-101817000	Weak transcription	Left Ventricle	heart
16	chr9:101807000-101831800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr9:101807200-101811400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr9:101807400-101811000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr9:101807400-101811600	Weak transcription	NHDF-Ad	bronchial
20	chr9:101807400-101814200	Weak transcription	Small Intestine	intestine
21	chr9:101807400-101819000	Strong transcription	Fetal Stomach	stomach
22	chr9:101807600-101810400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:101807600-101811800	Weak transcription	Lung	lung
24	chr9:101807600-101812000	Weak transcription	Aorta	Aorta
25	chr9:101807600-101831800	Strong transcription	Fetal Muscle Leg	muscle
26	chr9:101807800-101819800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr9:101808000-101809400	Genic enhancers	Stomach Smooth Muscle	stomach
28	chr9:101808200-101810000	Enhancers	K562	blood
29	chr9:101808400-101810800	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr9:101808400-101817200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:101808600-101809400	Enhancers	Colon Smooth Muscle	Colon
32	chr9:101808600-101809800	Enhancers	Rectal Smooth Muscle	rectum
33	chr9:101808600-101812600	Weak transcription	HSMMtube	muscle
34	chr9:101808800-101811200	Enhancers	Placenta	Placenta
35	chr9:101809000-101809600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr9:101809000-101811000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:101809200-101809600	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr9:101809200-101811200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr9:101809200-101812200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr9:101809200-101821600	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links