Variant report

Variant	rs9817900
Chromosome Location	chr3:134057650-134057651
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10755085	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs1111516	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11708815	0.86[ASN][1000 genomes]
rs11719057	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12495847	0.80[ASN][1000 genomes]
rs13075185	0.86[ASN][1000 genomes]
rs13084853	0.94[YRI][hapmap]
rs13322269	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs1353776	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1353777	0.80[ASN][1000 genomes]
rs1353778	0.89[CHB][hapmap]
rs1466827	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1498731	0.95[ASN][1000 genomes]
rs1603824	0.95[ASN][1000 genomes]
rs1863910	0.80[ASN][1000 genomes]
rs2133307	0.95[ASN][1000 genomes]
rs2400278	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2400279	0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2400280	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34341902	0.95[ASN][1000 genomes]
rs35951257	0.95[ASN][1000 genomes]
rs3732852	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3773820	0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3821705	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4264700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974485	0.95[ASN][1000 genomes]
rs4974486	1.00[JPT][hapmap]
rs4974487	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4974489	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974491	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974494	0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4974495	0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4974496	0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4974497	0.95[ASN][1000 genomes]
rs4974498	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6439477	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6439478	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6786148	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613066	0.86[ASN][1000 genomes]
rs9450	0.95[ASN][1000 genomes]
rs9853621	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9817900	RP11-375I20.6	cis	Thyroid	GTEx
rs9817900	STAG1	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134035000-134058800	Weak transcription	Liver	Liver
2	chr3:134042000-134060800	Enhancers	Placenta	Placenta
3	chr3:134049200-134060800	Enhancers	Fetal Intestine Large	intestine
4	chr3:134050600-134060400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:134050800-134061000	Weak transcription	Fetal Brain Female	brain
6	chr3:134051400-134058800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:134051400-134058800	Weak transcription	Fetal Kidney	kidney
8	chr3:134052200-134058600	Enhancers	Esophagus	oesophagus
9	chr3:134052800-134058600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:134052800-134058800	Enhancers	HepG2	liver
11	chr3:134053000-134061200	Enhancers	Adipose Nuclei	Adipose
12	chr3:134054000-134059600	Weak transcription	Colonic Mucosa	Colon
13	chr3:134054000-134064200	Weak transcription	Aorta	Aorta
14	chr3:134054200-134058200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:134054200-134060200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr3:134054200-134069800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:134054400-134069400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:134054600-134061000	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:134055200-134061400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:134055600-134059600	Weak transcription	HSMM	muscle
21	chr3:134055800-134058200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr3:134055800-134058800	Weak transcription	NHLF	lung
23	chr3:134055800-134059400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:134055800-134059600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:134055800-134071000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:134056000-134058400	Weak transcription	NHDF-Ad	bronchial
27	chr3:134056000-134058800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:134056000-134058800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:134056200-134058800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:134056200-134066600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr3:134056400-134058000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:134056400-134059000	Weak transcription	HSMMtube	muscle
33	chr3:134056400-134059600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:134056400-134059600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:134056400-134064800	Weak transcription	Ovary	ovary
36	chr3:134056600-134058200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:134056600-134059600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:134056600-134059800	Weak transcription	HMEC	breast
39	chr3:134056600-134060000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:134056600-134060000	Weak transcription	NHEK	skin
41	chr3:134056800-134058800	Weak transcription	Right Atrium	heart
42	chr3:134056800-134058800	Weak transcription	Osteobl	bone
43	chr3:134056800-134059000	Weak transcription	Left Ventricle	heart
44	chr3:134057000-134057800	Weak transcription	Gastric	stomach
45	chr3:134057000-134058000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:134057000-134058000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:134057000-134058200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:134057000-134058200	Weak transcription	Lung	lung
49	chr3:134057000-134058600	Weak transcription	Spleen	Spleen
50	chr3:134057000-134059000	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links