Variant report

Variant	rs10117457
Chromosome Location	chr9:96823684-96823685
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:96822397..96829591-chr9:96927085..96931647,12	MCF-7	breast:
2	chr9:96801741..96804913-chr9:96822695..96825395,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269946	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10122334	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10123954	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10429556	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10429603	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10435922	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10435924	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10739967	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10739969	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10761308	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10761309	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10761313	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10761315	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10821284	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10821285	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10821290	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10993037	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10993041	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12351292	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12684427	0.86[EUR][1000 genomes]
rs1316814	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1320547	0.87[EUR][1000 genomes]
rs13299545	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1331216	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1331217	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1331218	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1331219	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1343995	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1360429	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1411860	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1418251	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1576640	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1590969	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1592153	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1832857	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1854835	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1933668	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1933669	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1933679	0.87[EUR][1000 genomes]
rs2026917	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2094927	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2150625	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2153058	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2153070	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2153792	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2211362	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2225458	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2226117	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35883789	0.86[EUR][1000 genomes]
rs3847307	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3996241	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4282631	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4406469	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4744307	0.81[EUR][1000 genomes]
rs4744308	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744314	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744316	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6479522	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6479529	0.91[ASN][1000 genomes]
rs7033481	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7033898	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7045643	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7858069	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7867253	0.85[EUR][1000 genomes]
rs7867925	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs914295	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs914296	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs914297	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9299414	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs987511	0.91[EUR][1000 genomes];0.84[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	nsv893589	chr9:96624645-96884544	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv482457	chr9:96813852-96996170	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	217 gene(s)	inside rSNPs	diseases
3	nsv1043704	chr9:96816552-96873018	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96794200-96828000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:96795400-96823800	Weak transcription	Left Ventricle	heart
3	chr9:96818200-96823800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:96819000-96833400	Weak transcription	HSMM	muscle
5	chr9:96819200-96823800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr9:96819200-96824000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr9:96819400-96823800	Weak transcription	Aorta	Aorta
8	chr9:96819400-96828000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:96819400-96832800	Weak transcription	HSMMtube	muscle
10	chr9:96819600-96823800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:96819600-96823800	Weak transcription	NHEK	skin
12	chr9:96819600-96824000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:96819600-96827600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr9:96819600-96828000	Weak transcription	NHDF-Ad	bronchial
15	chr9:96820600-96836400	Weak transcription	Pancreas	Pancrea
16	chr9:96822400-96824000	Strong transcription	Fetal Lung	lung
17	chr9:96822400-96859800	Weak transcription	Psoas Muscle	Psoas
18	chr9:96822600-96832800	Weak transcription	Primary T cells from cord blood	blood
19	chr9:96822800-96824200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:96822800-96824800	ZNF genes & repeats	Fetal Stomach	stomach
21	chr9:96823000-96824000	Strong transcription	Right Ventricle	heart
22	chr9:96823000-96824200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr9:96823000-96824400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:96823000-96824400	ZNF genes & repeats	Fetal Intestine Large	intestine
25	chr9:96823000-96824600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
26	chr9:96823000-96824600	ZNF genes & repeats	Spleen	Spleen
27	chr9:96823000-96824800	ZNF genes & repeats	Fetal Muscle Leg	muscle
28	chr9:96823000-96825000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
29	chr9:96823400-96823800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:96823400-96824200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:96823400-96824200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr9:96823400-96824200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:96823400-96824800	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr9:96823600-96823800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr9:96823600-96824200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr9:96823600-96824400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr9:96823600-96824600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links