Variant report

Variant	rs9680
Chromosome Location	chr6:71570641-71570642
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11752509	0.92[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs13196394	0.92[CEU][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs13197338	0.92[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13198627	0.87[ASN][1000 genomes]
rs13202113	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13203355	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13212771	0.92[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17763077	0.92[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs2038477	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs2474915	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs2474921	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2504748	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs2504750	0.83[JPT][hapmap]
rs2504751	0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2504752	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs34336229	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34519120	0.89[EUR][1000 genomes]
rs35293093	0.89[EUR][1000 genomes]
rs3734371	0.83[LWK][hapmap];0.91[MKK][hapmap];0.86[EUR][1000 genomes]
rs3734372	0.83[LWK][hapmap];0.91[MKK][hapmap];0.86[EUR][1000 genomes]
rs483894	0.83[JPT][hapmap]

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	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9680	COL19A1	cis	parietal	SCAN
rs9680	B3GAT2	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71531200-71571000	Weak transcription	Stomach Mucosa	stomach
2	chr6:71537600-71574200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:71545400-71572200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr6:71549800-71573000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:71550000-71575400	Weak transcription	Ovary	ovary
6	chr6:71550600-71573000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:71551000-71571400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:71552400-71574200	Weak transcription	HSMM	muscle
9	chr6:71554400-71572800	Weak transcription	Thymus	Thymus
10	chr6:71554400-71572800	Weak transcription	Osteobl	bone
11	chr6:71554400-71574400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:71554600-71572800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:71556600-71571400	Weak transcription	Psoas Muscle	Psoas
14	chr6:71556600-71574400	Weak transcription	Fetal Intestine Small	intestine
15	chr6:71557000-71572800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:71557200-71572200	Weak transcription	Fetal Heart	heart
17	chr6:71558800-71575000	Weak transcription	HUVEC	blood vessel
18	chr6:71559000-71573800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr6:71559400-71573800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr6:71560600-71574200	Weak transcription	Brain Germinal Matrix	brain
21	chr6:71561200-71573000	Weak transcription	Brain Anterior Caudate	brain
22	chr6:71561200-71573400	Weak transcription	HMEC	breast
23	chr6:71561600-71574000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:71563400-71573600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:71563800-71571600	Weak transcription	HepG2	liver
26	chr6:71564000-71575800	Weak transcription	Right Ventricle	heart
27	chr6:71564400-71573000	Weak transcription	Spleen	Spleen
28	chr6:71564800-71572200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr6:71564800-71573000	Weak transcription	NH-A	brain
30	chr6:71566200-71571600	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr6:71566200-71572200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:71566400-71574200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:71566600-71571600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr6:71566600-71572000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:71566800-71571600	Strong transcription	Adipose Nuclei	Adipose
36	chr6:71566800-71572000	Strong transcription	Liver	Liver
37	chr6:71567000-71572000	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr6:71567000-71572000	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr6:71567000-71573000	Weak transcription	Brain Substantia Nigra	brain
40	chr6:71567200-71571400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:71567200-71571400	Strong transcription	Dnd41	blood
42	chr6:71567200-71571600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:71567200-71571600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr6:71567200-71571600	Strong transcription	Duodenum Mucosa	Duodenum
45	chr6:71567400-71571400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:71567400-71571800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr6:71567400-71572800	Weak transcription	Hela-S3	cervix
48	chr6:71567800-71571200	Weak transcription	Aorta	Aorta
49	chr6:71567800-71572800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:71568000-71571200	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links