Variant report

Variant	rs17010904
Chromosome Location	chr1:222008757-222008758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10495180	0.81[EUR][1000 genomes]
rs11118867	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12067828	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12090179	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3003899	0.92[CHB][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4846729	1.00[TSI][hapmap];0.87[YRI][hapmap]
rs59632580	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs60129776	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6604673	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73112693	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription 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	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221967400-222009800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:222000000-222010200	Enhancers	HMEC	breast
3	chr1:222000600-222019000	Weak transcription	Lung	lung
4	chr1:222000800-222009800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:222000800-222011000	Weak transcription	Thymus	Thymus
6	chr1:222001200-222011000	Weak transcription	Fetal Thymus	thymus
7	chr1:222001800-222009400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:222003400-222009200	Weak transcription	GM12878-XiMat	blood
9	chr1:222003600-222009800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:222004200-222011000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:222004200-222012800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:222004400-222011000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr1:222004600-222011200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:222004800-222009600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr1:222005600-222009400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:222005800-222019000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:222006200-222012600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:222006400-222011400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:222006800-222012600	Weak transcription	Esophagus	oesophagus
20	chr1:222007000-222010600	Enhancers	Hela-S3	cervix
21	chr1:222007600-222008800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:222007600-222011400	Weak transcription	HUVEC	blood vessel
23	chr1:222007800-222010000	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr1:222008000-222008800	Enhancers	Fetal Lung	lung
25	chr1:222008200-222009400	Enhancers	Liver	Liver
26	chr1:222008200-222013400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:222008400-222008800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr1:222008400-222009000	Enhancers	Placenta Amnion	Placenta Amnion
29	chr1:222008400-222009400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:222008400-222009400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:222008400-222012600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:222008600-222009600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:222008600-222012600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:222008600-222012600	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links