Variant report

Variant	rs10989162
Chromosome Location	chr9:103342342-103342343
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1000477	0.82[JPT][hapmap]
rs10465118	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs10465147	0.84[JPT][hapmap]
rs10465148	0.82[JPT][hapmap]
rs10465149	0.84[JPT][hapmap]
rs10512270	1.00[CEU][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap]
rs10512271	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap]
rs10819776	0.82[JPT][hapmap]
rs10819782	0.84[JPT][hapmap]
rs10819785	0.84[JPT][hapmap]
rs10819787	0.84[JPT][hapmap]
rs10819788	0.82[JPT][hapmap]
rs10819789	0.82[JPT][hapmap]
rs10819795	0.88[ASN][1000 genomes]
rs10989078	0.82[JPT][hapmap]
rs10989082	0.82[JPT][hapmap]
rs10989085	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap]
rs10989094	0.82[JPT][hapmap]
rs10989097	0.82[JPT][hapmap]
rs10989103	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap]
rs10989105	0.84[JPT][hapmap]
rs10989107	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs10989111	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap]
rs10989112	0.82[JPT][hapmap]
rs10989113	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap]
rs10989114	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap]
rs10989115	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap]
rs10989120	0.83[JPT][hapmap]
rs10989123	0.84[JPT][hapmap]
rs10989127	0.82[JPT][hapmap]
rs10989130	0.84[JPT][hapmap]
rs10989131	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs10989144	1.00[CEU][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap]
rs10989145	1.00[CEU][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap]
rs10989146	0.90[JPT][hapmap]
rs10989147	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs10989150	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs10989152	0.92[JPT][hapmap]
rs10989153	0.92[JPT][hapmap]
rs10989154	1.00[CEU][hapmap];0.92[JPT][hapmap];0.82[YRI][hapmap]
rs10989156	0.93[JPT][hapmap]
rs10989161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10989169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10989170	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10989173	0.95[ASN][1000 genomes]
rs10989174	0.89[ASN][1000 genomes]
rs11793014	0.84[JPT][hapmap]
rs12004257	0.82[JPT][hapmap]
rs12056981	1.00[CEU][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap]
rs12235981	0.92[JPT][hapmap]
rs12236071	1.00[CEU][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap]
rs12236970	0.92[JPT][hapmap]
rs12237481	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap]
rs12238560	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap]
rs12683122	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap]
rs12683548	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs12683889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12684438	0.82[JPT][hapmap]
rs12684454	0.84[JPT][hapmap]
rs12685564	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1332598	0.82[JPT][hapmap]
rs16919174	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs16919204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16919211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1930246	0.82[JPT][hapmap]
rs1931140	0.93[JPT][hapmap]
rs2026423	0.82[JPT][hapmap]
rs2069236	0.82[JPT][hapmap]
rs2151106	0.84[JPT][hapmap]
rs2183989	0.84[JPT][hapmap]
rs2183990	0.84[JPT][hapmap]
rs2183991	0.84[JPT][hapmap]
rs2274881	1.00[CEU][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap]
rs2274882	0.82[JPT][hapmap]
rs28623148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4454331	0.95[ASN][1000 genomes]
rs55757829	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56290508	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56354846	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7021028	0.92[JPT][hapmap]
rs7028822	0.82[JPT][hapmap]
rs7029001	0.84[JPT][hapmap]
rs7042669	0.84[JPT][hapmap]
rs7046659	0.82[JPT][hapmap]
rs72735197	0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103307400-103347800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:103308600-103345400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:103311800-103342400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr9:103318400-103342400	Weak transcription	Brain Anterior Caudate	brain
5	chr9:103318600-103344000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr9:103324800-103345400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:103327800-103349400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:103329600-103360800	Weak transcription	Aorta	Aorta
9	chr9:103329800-103351800	Weak transcription	Ovary	ovary
10	chr9:103330000-103357800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr9:103330400-103345400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:103330400-103351600	Weak transcription	Fetal Stomach	stomach
13	chr9:103330800-103349400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr9:103331600-103360200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr9:103332400-103351600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:103332400-103357600	Weak transcription	Fetal Lung	lung
17	chr9:103333600-103360800	Weak transcription	Fetal Brain Male	brain
18	chr9:103334200-103351000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr9:103334600-103350600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr9:103334800-103350200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:103335000-103351000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr9:103336800-103347800	Weak transcription	Brain Germinal Matrix	brain
23	chr9:103337400-103342800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:103337600-103352200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr9:103338600-103348000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr9:103338800-103352200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr9:103339600-103344600	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr9:103340000-103342600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr9:103340000-103344400	Active TSS	HSMMtube	muscle
30	chr9:103340000-103344600	Active TSS	Fetal Muscle Leg	muscle
31	chr9:103340000-103344600	Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr9:103340200-103344200	Active TSS	Right Atrium	heart
33	chr9:103340200-103344400	Active TSS	Right Ventricle	heart
34	chr9:103340200-103344800	Active TSS	Fetal Muscle Trunk	muscle
35	chr9:103340400-103344000	Active TSS	Fetal Heart	heart
36	chr9:103340600-103342400	Active TSS	HSMM	muscle
37	chr9:103340600-103342400	Enhancers	Osteobl	bone
38	chr9:103340600-103345200	Weak transcription	Fetal Brain Female	brain
39	chr9:103340600-103351800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr9:103340800-103342400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr9:103340800-103351400	Weak transcription	NHDF-Ad	bronchial
42	chr9:103341000-103343000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:103341000-103351400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr9:103341200-103342400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr9:103341200-103342400	Weak transcription	Brain Hippocampus Middle	brain
46	chr9:103341200-103343200	Weak transcription	Brain Substantia Nigra	brain
47	chr9:103341200-103344400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr9:103341200-103345000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr9:103341400-103342600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr9:103341600-103342600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links