Variant report

Variant	rs7873162
Chromosome Location	chr9:95983986-95983987
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95982340..95984342-chr9:96001174..96003996,2	K562	blood:
2	chr9:95976952..95979660-chr9:95981802..95984086,2	MCF-7	breast:
3	chr9:95983716..95985400-chr9:96057478..96060069,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10992681	1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1107614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1107615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11787888	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11793893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12001073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12002458	0.83[AMR][1000 genomes]
rs13287544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13290796	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13301530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34085543	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34834050	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35199621	0.83[AMR][1000 genomes]
rs35438673	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4329328	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6479471	0.92[TSI][hapmap]
rs6479474	0.85[MEX][hapmap];0.87[TSI][hapmap]
rs7019910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022051	0.85[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes]
rs7042943	0.85[MEX][hapmap];0.92[TSI][hapmap]
rs7046965	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7855391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857220	0.92[TSI][hapmap]
rs7867954	0.83[AMR][1000 genomes]
rs7874101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7873162	SECISBP2	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95955800-95985600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:95971200-95985800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr9:95974200-95985400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:95974400-95986800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr9:95978800-95985400	Weak transcription	Brain Germinal Matrix	brain
6	chr9:95979600-95986400	Enhancers	Fetal Heart	heart
7	chr9:95979600-95992200	Enhancers	Left Ventricle	heart
8	chr9:95979800-95984800	Enhancers	Right Ventricle	heart
9	chr9:95980000-95985400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr9:95980000-95985600	Weak transcription	HepG2	liver
11	chr9:95980200-95985400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:95980200-95985600	Weak transcription	Small Intestine	intestine
13	chr9:95980600-95985400	Weak transcription	Fetal Intestine Large	intestine
14	chr9:95980600-95985400	Strong transcription	Fetal Intestine Small	intestine
15	chr9:95980600-95985400	Weak transcription	Right Atrium	heart
16	chr9:95981400-95985400	Weak transcription	Colon Smooth Muscle	Colon
17	chr9:95981600-95989200	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr9:95981800-95985600	Weak transcription	Brain Anterior Caudate	brain
19	chr9:95982000-95984600	Weak transcription	Hela-S3	cervix
20	chr9:95982400-95985400	Weak transcription	Gastric	stomach
21	chr9:95982400-95985400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr9:95982600-95985600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr9:95982600-95986800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr9:95982800-95985200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr9:95982800-95985200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr9:95982800-95985400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr9:95982800-95985400	Weak transcription	Colonic Mucosa	Colon
28	chr9:95983000-95984400	Enhancers	Fetal Muscle Leg	muscle
29	chr9:95983000-95985200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr9:95983000-95985600	Weak transcription	Brain Hippocampus Middle	brain
31	chr9:95983200-95984200	Enhancers	Fetal Brain Male	brain
32	chr9:95983200-95987200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
33	chr9:95983600-95985400	Weak transcription	Psoas Muscle	Psoas
34	chr9:95983600-95985800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr9:95983800-95984200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr9:95983800-95984800	Weak transcription	Pancreas	Pancrea
37	chr9:95983800-95985600	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links