Variant report

Variant	rs1854909
Chromosome Location	chr9:13160322-13160323
allele	G/T
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:65)

rs_ID	r²[population]
rs10116304	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10116749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10122431	0.92[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10125770	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10511577	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10733254	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10738323	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10738324	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10738325	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10756454	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10756455	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10756456	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10756457	0.96[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10756458	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10756459	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10756460	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10756461	0.80[TSI][hapmap]
rs10809906	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs10809907	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10809908	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10809912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10809913	0.86[ASN][1000 genomes]
rs10809920	0.86[JPT][hapmap]
rs10960955	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10960958	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10960959	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12351444	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1330129	0.95[JPT][hapmap]
rs1331668	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1331670	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1331672	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1331673	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1331674	0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1331675	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1360058	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1556421	0.84[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16930137	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1854414	0.87[EUR][1000 genomes]
rs1854907	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1854908	0.96[CEU][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1929541	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1999393	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2225483	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2274856	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2297003	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35068818	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3818595	0.83[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4237130	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4741291	0.83[AMR][1000 genomes]
rs58794982	0.88[ASN][1000 genomes]
rs6474753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6474754	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6474755	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024892	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7035244	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7037618	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7037704	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7039646	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7040347	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72706366	0.89[ASN][1000 genomes]
rs7859465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7867993	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7871112	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7871575	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9886797	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.83[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	nsv892578	chr9:12942956-13485035	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:13103200-13163400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:13103200-13175600	Weak transcription	HepG2	liver
3	chr9:13121600-13225200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr9:13122600-13186400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:13135400-13223600	Weak transcription	Lung	lung
6	chr9:13136000-13192400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:13138200-13161000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:13138800-13191800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr9:13139000-13188200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr9:13139800-13174800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr9:13140200-13161200	Weak transcription	Fetal Stomach	stomach
12	chr9:13140200-13167800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr9:13140200-13174800	Weak transcription	Right Ventricle	heart
14	chr9:13141000-13181600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:13141000-13197800	Weak transcription	NHDF-Ad	bronchial
16	chr9:13141200-13188200	Weak transcription	NHLF	lung
17	chr9:13143600-13202200	Weak transcription	Pancreas	Pancrea
18	chr9:13143800-13164800	Weak transcription	Fetal Brain Female	brain
19	chr9:13143800-13167800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr9:13145000-13161600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr9:13145400-13163600	Weak transcription	Brain Hippocampus Middle	brain
22	chr9:13145400-13163600	Weak transcription	Brain Substantia Nigra	brain
23	chr9:13145400-13203200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr9:13145400-13228600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr9:13145600-13163400	Weak transcription	Brain Germinal Matrix	brain
26	chr9:13146200-13163000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:13146600-13202400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr9:13147000-13178000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:13147800-13167000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr9:13148000-13167600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr9:13148200-13167600	Weak transcription	NH-A	brain
32	chr9:13149000-13163400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:13150000-13160800	Weak transcription	Brain Angular Gyrus	brain
34	chr9:13150000-13167400	Weak transcription	HSMMtube	muscle
35	chr9:13150000-13193200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr9:13150400-13180800	Weak transcription	A549	lung
37	chr9:13152400-13163000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:13153000-13167800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr9:13153200-13163000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr9:13153200-13194800	Weak transcription	Fetal Kidney	kidney
41	chr9:13153800-13167800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr9:13154600-13161200	Weak transcription	Fetal Intestine Small	intestine
43	chr9:13154800-13161000	Weak transcription	Fetal Intestine Large	intestine
44	chr9:13154800-13167000	Weak transcription	Colon Smooth Muscle	Colon
45	chr9:13155400-13161200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:13155800-13162800	Strong transcription	Liver	Liver
47	chr9:13156600-13161000	Weak transcription	Fetal Muscle Leg	muscle
48	chr9:13156800-13160600	Strong transcription	HSMM	muscle
49	chr9:13156800-13201400	Weak transcription	Psoas Muscle	Psoas
50	chr9:13157400-13175400	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links