Variant report

Variant	rs6663943
Chromosome Location	chr1:62741309-62741310
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10889317	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs11207949	0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs12037540	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs12044289	0.85[EUR][1000 genomes]
rs12082623	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs1325742	0.85[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs1886831	0.91[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs1886832	0.91[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs2666483	0.80[ASW][hapmap];0.82[LWK][hapmap];0.85[EUR][1000 genomes]
rs2666501	0.82[EUR][1000 genomes]
rs2666502	0.85[EUR][1000 genomes]
rs2765265	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs2765267	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs3844053	0.82[CEU][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3844054	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs3850631	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4915811	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs4915812	0.86[CEU][hapmap]
rs6587965	0.90[EUR][1000 genomes]
rs7413419	0.80[EUR][1000 genomes]
rs7413420	0.80[EUR][1000 genomes]
rs7551135	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62732400-62748400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:62734200-62750800	Weak transcription	Gastric	stomach
3	chr1:62737600-62741800	Strong transcription	Placenta	Placenta
4	chr1:62737800-62742600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:62737800-62744400	Weak transcription	Fetal Intestine Large	intestine
6	chr1:62738000-62749000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:62738200-62746400	Weak transcription	Fetal Kidney	kidney
8	chr1:62738200-62751200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:62739600-62744200	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr1:62740200-62746400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:62740400-62743200	Weak transcription	Liver	Liver
12	chr1:62740400-62744600	Weak transcription	Fetal Thymus	thymus
13	chr1:62740400-62745400	Weak transcription	Fetal Lung	lung
14	chr1:62740400-62746600	Weak transcription	Pancreas	Pancrea
15	chr1:62740600-62741800	Enhancers	Fetal Muscle Leg	muscle
16	chr1:62740600-62743000	Weak transcription	Fetal Intestine Small	intestine
17	chr1:62740600-62744400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:62740600-62744600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:62740600-62744600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr1:62740800-62741400	Enhancers	Adipose Nuclei	Adipose
21	chr1:62740800-62742800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:62741000-62741400	Enhancers	Brain Germinal Matrix	brain
23	chr1:62741000-62745000	Weak transcription	HepG2	liver
24	chr1:62741200-62743200	Weak transcription	Fetal Stomach	stomach
25	chr1:62741200-62744400	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links