Variant report

Variant	rs7035385
Chromosome Location	chr9:79019066-79019067
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79008991..79011604-chr9:79014498..79020251,6	K562	blood:
2	chr9:79008388..79010623-chr9:79018392..79020110,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135002	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10116800	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118954	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119732	0.95[ASN][1000 genomes]
rs10125012	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125667	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10781358	1.00[ASN][1000 genomes]
rs10781359	0.95[ASN][1000 genomes]
rs10781360	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10869770	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10869771	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10869774	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11144870	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11144875	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144878	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144881	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144887	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144894	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11144897	0.95[ASN][1000 genomes]
rs1129399	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11548954	0.89[ASN][1000 genomes]
rs11791951	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793613	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11794019	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12156473	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12375735	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12377856	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12377878	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12380332	0.84[ASN][1000 genomes]
rs12380522	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1324212	1.00[CHB][hapmap]
rs1324213	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951910	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2251604	0.84[AFR][1000 genomes]
rs2377640	0.91[AMR][1000 genomes]
rs2377641	0.96[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3187236	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4571791	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55740812	0.94[ASN][1000 genomes]
rs57339182	0.84[ASN][1000 genomes]
rs57480680	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58136435	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59424752	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61334567	0.91[AMR][1000 genomes]
rs62564441	0.90[ASN][1000 genomes]
rs62564442	0.90[ASN][1000 genomes]
rs62564446	0.84[ASN][1000 genomes]
rs62565109	0.83[ASN][1000 genomes]
rs62567918	0.94[ASN][1000 genomes]
rs62567919	0.89[ASN][1000 genomes]
rs62568690	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62568692	1.00[ASN][1000 genomes]
rs6560513	0.91[AMR][1000 genomes]
rs6560515	0.82[ASW][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes]
rs6560516	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7023191	0.82[CEU][hapmap];0.85[CHB][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7025942	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7026067	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029439	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037345	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7038009	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7038056	0.90[ASN][1000 genomes]
rs7040138	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041690	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047489	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7049245	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851616	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7852884	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7853410	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7854540	0.84[ASN][1000 genomes]
rs7859327	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875575	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[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	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893478	chr9:78933874-79101006	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7035385	VPS13A	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79010600-79019400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:79015200-79019600	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr9:79016000-79023000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:79016800-79019600	Enhancers	Liver	Liver
5	chr9:79016800-79020000	Enhancers	Fetal Intestine Small	intestine
6	chr9:79017800-79019800	Enhancers	Fetal Intestine Large	intestine
7	chr9:79018600-79019600	Enhancers	GM12878-XiMat	blood
8	chr9:79018800-79019200	Enhancers	Rectal Mucosa Donor 29	rectum
9	chr9:79018800-79019200	Enhancers	HUVEC	blood vessel
10	chr9:79018800-79019200	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr9:79018800-79020200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:79019000-79019200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:79019000-79019200	Enhancers	NHDF-Ad	bronchial
14	chr9:79019000-79020400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr9:79019000-79027600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links