Variant report

Variant	rs10780561
Chromosome Location	chr9:85602892-85602893
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1008171	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1010480	0.92[CEU][hapmap]
rs10116216	0.87[CEU][hapmap]
rs10116254	0.92[CEU][hapmap]
rs10121204	0.91[CEU][hapmap]
rs10121376	0.91[EUR][1000 genomes]
rs10121395	0.92[CEU][hapmap]
rs10735559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780562	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10780563	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs10780564	0.95[EUR][1000 genomes]
rs10780565	0.92[CEU][hapmap]
rs10780567	0.91[CEU][hapmap]
rs10867928	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs10867929	0.91[CEU][hapmap]
rs10867930	0.92[CEU][hapmap]
rs1125915	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs1393562	0.92[CEU][hapmap]
rs1393563	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1393564	0.84[CEU][hapmap]
rs1393565	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1502682	0.91[CEU][hapmap]
rs1502683	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1502684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1502685	0.92[CEU][hapmap]
rs1546315	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs1546316	0.92[CEU][hapmap]
rs1546317	0.92[CEU][hapmap]
rs1580881	0.92[CEU][hapmap]
rs1976455	0.91[CEU][hapmap]
rs1995423	0.87[CEU][hapmap]
rs2062761	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2279814	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4146960	0.91[CEU][hapmap]
rs4146961	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs4301515	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs4348583	0.91[CEU][hapmap]
rs4355855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4385545	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4391505	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4460464	0.87[CEU][hapmap]
rs4623517	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4877244	0.92[CEU][hapmap]
rs4877724	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4877725	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4877726	0.88[CEU][hapmap]
rs6559693	0.91[EUR][1000 genomes]
rs6559694	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs6559695	1.00[CEU][hapmap]
rs7019227	0.91[CEU][hapmap]
rs7024864	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7847666	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs7849126	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7853052	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7854101	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs7862012	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7864688	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866666	0.91[CEU][hapmap]
rs7867614	0.84[EUR][1000 genomes]
rs7872982	0.86[EUR][1000 genomes]
rs871512	0.87[CEU][hapmap]
rs952450	0.92[CEU][hapmap]
rs998119	0.81[EUR][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	nsv1050771	chr9:85416931-85643417	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv893511	chr9:85495968-85833127	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv6585	chr9:85566659-85611489	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85592800-85608600	Weak transcription	Stomach Mucosa	stomach
2	chr9:85594600-85606000	Weak transcription	Fetal Intestine Large	intestine
3	chr9:85594800-85628200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:85597200-85627000	Weak transcription	A549	lung
5	chr9:85597600-85608600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:85597600-85608600	Weak transcription	HMEC	breast
7	chr9:85600800-85604200	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr9:85601600-85603400	Enhancers	Rectal Mucosa Donor 29	rectum
9	chr9:85601800-85603000	Enhancers	Fetal Intestine Small	intestine
10	chr9:85601800-85604400	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr9:85602400-85603000	Enhancers	Fetal Stomach	stomach
12	chr9:85602400-85603200	Enhancers	Duodenum Mucosa	Duodenum
13	chr9:85602800-85603000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:85602800-85603000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr9:85602800-85603000	Genic enhancers	Esophagus	oesophagus
16	chr9:85602800-85603000	Enhancers	Fetal Kidney	kidney
17	chr9:85602800-85603000	Genic enhancers	Gastric	stomach
18	chr9:85602800-85603800	Genic enhancers	Pancreas	Pancrea
19	chr9:85602800-85604000	Enhancers	Ovary	ovary

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