Variant report

Variant	rs2666508
Chromosome Location	chr1:62740930-62740931
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10493320	0.82[AMR][1000 genomes]
rs12063531	0.82[GIH][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs12078087	0.82[AMR][1000 genomes]
rs12079207	0.82[AMR][1000 genomes]
rs12718429	0.82[AMR][1000 genomes]
rs12760895	0.82[GIH][hapmap];0.80[MEX][hapmap]
rs1555833	0.80[ASN][1000 genomes]
rs2258470	0.90[JPT][hapmap]
rs2260581	0.90[JPT][hapmap]
rs2262106	0.90[JPT][hapmap]
rs2262110	0.90[JPT][hapmap]
rs2666472	0.90[JPT][hapmap]
rs2666473	0.90[JPT][hapmap]
rs2666474	0.90[JPT][hapmap]
rs2666487	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2666488	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2666503	1.00[ASW][hapmap];0.90[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2666506	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765241	0.90[JPT][hapmap]
rs2765244	0.90[JPT][hapmap]
rs2765247	0.90[JPT][hapmap]
rs2765248	0.90[JPT][hapmap]
rs2765249	0.90[JPT][hapmap]
rs2765250	0.82[ASN][1000 genomes]
rs2765251	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2765258	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2765261	0.81[CEU][hapmap]
rs2765270	0.89[JPT][hapmap]
rs34752481	0.88[AMR][1000 genomes]
rs7516290	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7520614	0.81[CEU][hapmap]
rs765691	0.81[CEU][hapmap]
rs765692	0.81[CEU][hapmap];0.82[MEX][hapmap]
rs912894	0.82[AMR][1000 genomes]
rs912895	0.82[AMR][1000 genomes]
rs912896	0.82[AMR][1000 genomes]
rs958803	0.89[JPT][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2666508	DAB1	cis	cerebellum	SCAN

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	chr1:62733000-62741000	Weak transcription	Brain Germinal Matrix	brain
3	chr1:62734200-62750800	Weak transcription	Gastric	stomach
4	chr1:62736400-62741000	Strong transcription	HepG2	liver
5	chr1:62737600-62741800	Strong transcription	Placenta	Placenta
6	chr1:62737800-62742600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:62737800-62744400	Weak transcription	Fetal Intestine Large	intestine
8	chr1:62738000-62749000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:62738200-62746400	Weak transcription	Fetal Kidney	kidney
10	chr1:62738200-62751200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:62739600-62744200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr1:62740000-62741200	Enhancers	Fetal Heart	heart
13	chr1:62740200-62746400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:62740400-62743200	Weak transcription	Liver	Liver
15	chr1:62740400-62744600	Weak transcription	Fetal Thymus	thymus
16	chr1:62740400-62745400	Weak transcription	Fetal Lung	lung
17	chr1:62740400-62746600	Weak transcription	Pancreas	Pancrea
18	chr1:62740600-62741800	Enhancers	Fetal Muscle Leg	muscle
19	chr1:62740600-62743000	Weak transcription	Fetal Intestine Small	intestine
20	chr1:62740600-62744400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:62740600-62744600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:62740600-62744600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:62740800-62741200	Enhancers	Fetal Stomach	stomach
24	chr1:62740800-62741400	Enhancers	Adipose Nuclei	Adipose
25	chr1:62740800-62742800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links