Variant report

Variant	rs3761199
Chromosome Location	chr20:30062456-30062457
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1006459	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11699147	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs1543438	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs2076373	0.86[CHB][hapmap]
rs2180566	0.86[CHB][hapmap]
rs2206383	0.81[CHB][hapmap]
rs2233832	0.95[CHB][hapmap];0.91[CHD][hapmap];0.81[ASN][1000 genomes]
rs2273468	0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[YRI][hapmap]
rs2281554	0.85[CHB][hapmap]
rs2295500	0.82[YRI][hapmap]
rs2376858	0.85[CHB][hapmap]
rs34267307	0.95[ASN][1000 genomes]
rs3861819	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs412142	0.83[JPT][hapmap]
rs4911306	0.90[CHB][hapmap]
rs4911328	0.82[YRI][hapmap]
rs4911329	0.86[CHB][hapmap]
rs6057888	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6059128	0.85[CHB][hapmap]
rs6059335	0.86[CHB][hapmap]
rs6059379	0.86[CHB][hapmap]
rs6059425	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6059434	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6059440	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6087445	0.86[CHB][hapmap]
rs6087464	0.86[CHB][hapmap]
rs6087468	0.86[CHB][hapmap];0.82[YRI][hapmap]
rs6088109	0.86[CHB][hapmap]
rs6088112	0.86[CHB][hapmap]
rs6088144	0.86[CHB][hapmap];0.82[YRI][hapmap]
rs6088215	0.86[CHB][hapmap]
rs6141934	0.86[CHB][hapmap]
rs66974934	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709045	0.82[YRI][hapmap]
rs734418	0.86[CHB][hapmap];0.82[YRI][hapmap]
rs760996	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869384	chr20:29833386-30605088	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	419 gene(s)	inside rSNPs	diseases
2	nsv470546	chr20:29833609-30235302	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	385 gene(s)	inside rSNPs	diseases
3	nsv1055527	chr20:29833958-30078925	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1062069	chr20:29833958-30153486	Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv1062612	chr20:29833958-30219337	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	383 gene(s)	inside rSNPs	diseases
6	nsv1061673	chr20:29833958-30649496	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	422 gene(s)	inside rSNPs	diseases
7	nsv544232	chr20:29833958-30649496	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	422 gene(s)	inside rSNPs	diseases
8	nsv1058344	chr20:29835037-30386611	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	402 gene(s)	inside rSNPs	diseases
9	nsv1059672	chr20:29835037-30621271	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	419 gene(s)	inside rSNPs	diseases
10	esv2763228	chr20:29835049-30239522	Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	385 gene(s)	inside rSNPs	diseases
11	nsv949085	chr20:29846303-30473188	Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	414 gene(s)	inside rSNPs	diseases
12	nsv1058639	chr20:29877877-30101083	Weak transcription Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
13	nsv544235	chr20:29877877-30101083	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
14	nsv1058020	chr20:29877877-30197681	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
15	nsv544236	chr20:29877877-30197681	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
16	nsv1063560	chr20:29877877-30435888	Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
17	nsv544237	chr20:29877877-30435888	Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
18	nsv458961	chr20:29893501-30275906	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	383 gene(s)	inside rSNPs	diseases
19	nsv585911	chr20:29893501-30275906	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	383 gene(s)	inside rSNPs	diseases
20	nsv1067177	chr20:29900572-30299363	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	383 gene(s)	inside rSNPs	diseases
21	nsv1067419	chr20:30029545-30162261	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
22	nsv544238	chr20:30029545-30162261	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3761199	PDXK	trans	multi-tissue	Pritchard
rs3761199	FRG1B	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:30059600-30063200	Weak transcription	Gastric	stomach
2	chr20:30060600-30062600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr20:30060800-30063000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr20:30061400-30063400	Enhancers	GM12878-XiMat	blood
5	chr20:30061600-30063200	Enhancers	Primary B cells from peripheral blood	blood
6	chr20:30061800-30063600	Enhancers	Primary B cells from cord blood	blood
7	chr20:30062000-30062600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr20:30062000-30062600	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr20:30062000-30062600	Bivalent Enhancer	Fetal Stomach	stomach
10	chr20:30062000-30062600	Enhancers	Right Atrium	heart
11	chr20:30062000-30062600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
12	chr20:30062000-30062800	Enhancers	Placenta	Placenta
13	chr20:30062000-30062800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
14	chr20:30062000-30063000	Weak transcription	A549	lung
15	chr20:30062200-30062600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr20:30062200-30062600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
17	chr20:30062200-30062600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr20:30062200-30062600	Bivalent Enhancer	Brain Hippocampus Middle	brain
19	chr20:30062200-30062600	Bivalent Enhancer	Fetal Lung	lung
20	chr20:30062200-30062600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
21	chr20:30062200-30062600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
22	chr20:30062200-30063000	Bivalent Enhancer	Esophagus	oesophagus
23	chr20:30062200-30063200	Enhancers	Lung	lung
24	chr20:30062200-30063400	Active TSS	Rectal Smooth Muscle	rectum
25	chr20:30062200-30063800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
26	chr20:30062400-30062600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
27	chr20:30062400-30062600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr20:30062400-30062800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
29	chr20:30062400-30062800	Weak transcription	Ovary	ovary
30	chr20:30062400-30062800	Weak transcription	Spleen	Spleen
31	chr20:30062400-30063200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
32	chr20:30062400-30064000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links