Variant report

Variant	rs11207949
Chromosome Location	chr1:62732421-62732422
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10889317	0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs12037540	0.82[EUR][1000 genomes]
rs12044289	0.82[EUR][1000 genomes]
rs12082623	0.82[EUR][1000 genomes]
rs12095173	0.85[JPT][hapmap]
rs1325742	0.82[EUR][1000 genomes]
rs1886831	0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs1886832	0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs2666483	0.90[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2666501	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2666502	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3844053	0.83[ASW][hapmap];0.88[LWK][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3844054	0.86[EUR][1000 genomes]
rs3850631	0.80[EUR][1000 genomes]
rs3895339	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4915609	0.81[JPT][hapmap]
rs4915811	0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs6587965	0.86[EUR][1000 genomes]
rs6663943	0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs7551135	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[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	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
5	esv3408127	chr1:62729964-62734262	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62711600-62737200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:62721000-62739400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:62728000-62734800	Weak transcription	Fetal Brain Male	brain
4	chr1:62729000-62737600	Weak transcription	Right Atrium	heart
5	chr1:62729400-62732600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:62729400-62734400	Strong transcription	Placenta Amnion	Placenta Amnion
7	chr1:62729600-62734000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:62729600-62736800	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:62729600-62737400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:62729600-62737400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:62729600-62737600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:62729600-62737800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:62729800-62737400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:62730800-62734000	Strong transcription	Adipose Nuclei	Adipose
15	chr1:62731400-62734600	Strong transcription	Fetal Muscle Trunk	muscle
16	chr1:62731400-62734800	Strong transcription	HepG2	liver
17	chr1:62731800-62732800	Strong transcription	Fetal Intestine Small	intestine
18	chr1:62731800-62733200	Genic enhancers	Pancreas	Pancrea
19	chr1:62732000-62734000	Genic enhancers	Fetal Stomach	stomach
20	chr1:62732000-62734800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:62732000-62734800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:62732200-62732600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:62732200-62733000	Enhancers	Brain Germinal Matrix	brain
24	chr1:62732200-62737000	Weak transcription	Esophagus	oesophagus
25	chr1:62732200-62737600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:62732400-62732600	Weak transcription	Fetal Lung	lung
27	chr1:62732400-62733800	Weak transcription	Gastric	stomach
28	chr1:62732400-62734200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:62732400-62737000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:62732400-62737400	Weak transcription	Fetal Kidney	kidney
31	chr1:62732400-62737600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr1:62732400-62737600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:62732400-62737600	Weak transcription	Placenta	Placenta
34	chr1:62732400-62740000	Weak transcription	Liver	Liver
35	chr1:62732400-62748400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links