Variant report

Variant	rs9857908
Chromosome Location	chr3:137835746-137835747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1107422	0.89[ASN][1000 genomes]
rs11719358	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs13100360	0.92[ASN][1000 genomes]
rs1351446	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1545816	0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1564496	0.95[ASN][1000 genomes]
rs17838821	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs179282	0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs2170309	0.93[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[ASN][1000 genomes]
rs2246945	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2622695	0.83[GIH][hapmap]
rs2622697	0.95[ASN][1000 genomes]
rs2622698	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2622704	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs2622705	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2622706	0.84[ASN][1000 genomes]
rs2622707	0.84[ASN][1000 genomes]
rs2622709	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2622710	0.87[ASN][1000 genomes]
rs2622711	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2622714	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2622715	0.91[ASN][1000 genomes]
rs2622716	0.91[ASN][1000 genomes]
rs2622717	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2622718	0.91[ASN][1000 genomes]
rs2622719	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2622720	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2622727	0.92[ASN][1000 genomes]
rs2622728	0.92[ASN][1000 genomes]
rs2622729	0.92[ASN][1000 genomes]
rs2622730	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2622745	0.88[ASN][1000 genomes]
rs2622746	0.99[ASN][1000 genomes]
rs2724679	0.90[ASN][1000 genomes]
rs2724687	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2724693	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[ASN][1000 genomes]
rs2724694	0.86[ASN][1000 genomes]
rs2724695	0.84[ASN][1000 genomes]
rs2724697	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2724698	0.84[ASN][1000 genomes]
rs2724699	0.84[ASN][1000 genomes]
rs2724700	0.84[ASN][1000 genomes]
rs2724701	0.84[ASN][1000 genomes]
rs2724702	0.84[ASN][1000 genomes]
rs2724703	0.81[ASN][1000 genomes]
rs2724704	0.84[ASN][1000 genomes]
rs2724705	0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2724706	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2724707	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2724708	0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2724716	0.92[ASN][1000 genomes]
rs2724717	0.89[ASN][1000 genomes]
rs2724729	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.88[MKK][hapmap];0.99[ASN][1000 genomes]
rs28480035	0.88[ASN][1000 genomes]
rs329381	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs329382	0.84[ASN][1000 genomes]
rs329383	0.91[ASN][1000 genomes]
rs329384	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs329385	0.92[ASN][1000 genomes]
rs329388	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs329389	0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs329390	0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs329391	0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs365504	0.80[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs367439	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs374045	0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs382629	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs384828	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs390729	0.89[ASN][1000 genomes]
rs405265	0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs405602	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs407009	0.84[ASN][1000 genomes]
rs419075	0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs425938	0.81[ASN][1000 genomes]
rs442800	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs445025	0.81[ASN][1000 genomes]
rs446644	0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs452195	0.84[ASN][1000 genomes]
rs453023	0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4678403	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs618553	0.87[ASN][1000 genomes]
rs6809258	0.88[ASN][1000 genomes]
rs7613955	0.89[ASN][1000 genomes]
rs7629243	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7639197	0.91[ASN][1000 genomes]
rs899983	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9812778	0.98[ASN][1000 genomes]
rs9834462	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9842648	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842918	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9860229	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9860630	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9874211	0.92[ASN][1000 genomes]
rs996432	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2757890	chr3:137611789-137933835	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2759180	chr3:137611789-137933835	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2751978	chr3:137715302-137890750	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1007857	chr3:137767454-137843106	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9857908	A4GNT	cis	Thyroid	GTEx
rs9857908	A4GNT	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137834800-137835800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:137834800-137835800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:137834800-137837400	Weak transcription	Pancreas	Pancrea
4	chr3:137834800-137837600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:137834800-137837600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:137834800-137837600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:137834800-137837600	Weak transcription	HSMM	muscle
8	chr3:137834800-137837800	Weak transcription	Spleen	Spleen
9	chr3:137834800-137843000	Weak transcription	Placenta	Placenta
10	chr3:137834800-137843600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:137835000-137835800	Enhancers	H9 Cell Line	embryonic stem cell
12	chr3:137835000-137837600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:137835000-137837600	Weak transcription	Stomach Mucosa	stomach
14	chr3:137835000-137837600	Weak transcription	HMEC	breast
15	chr3:137835000-137843600	Weak transcription	Right Ventricle	heart
16	chr3:137835200-137835800	Enhancers	H1 Cell Line	embryonic stem cell
17	chr3:137835200-137835800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr3:137835200-137835800	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr3:137835200-137835800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:137835200-137836000	Enhancers	Adipose Nuclei	Adipose
21	chr3:137835200-137836800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:137835200-137837200	Weak transcription	Fetal Kidney	kidney
23	chr3:137835200-137837400	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:137835200-137837400	Weak transcription	NHDF-Ad	bronchial
25	chr3:137835200-137837600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:137835200-137837600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:137835200-137837600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:137835200-137837600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr3:137835200-137837600	Weak transcription	Fetal Stomach	stomach
30	chr3:137835200-137843200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr3:137835200-137843600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:137835200-137843600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:137835200-137843600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:137835400-137837400	Weak transcription	NHLF	lung
35	chr3:137835400-137837400	Weak transcription	Osteobl	bone
36	chr3:137835400-137837600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:137835400-137837600	Weak transcription	Hela-S3	cervix
38	chr3:137835400-137843400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:137835400-137844200	Weak transcription	A549	lung
40	chr3:137835600-137835800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:137835600-137835800	Enhancers	Aorta	Aorta
42	chr3:137835600-137835800	Enhancers	Fetal Heart	heart
43	chr3:137835600-137836000	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr3:137835600-137837000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:137835600-137837400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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