Variant report

Variant	rs3923574
Chromosome Location	chrX:80000302-80000303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11796018	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs12556865	0.88[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs16979508	0.93[CEU][hapmap];0.96[GIH][hapmap]
rs2137444	0.88[YRI][hapmap]
rs28417201	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs3106407	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3122406	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs3123257	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3132154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs3810676	0.82[JPT][hapmap]
rs4240018	1.00[CEU][hapmap]
rs4567187	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap]
rs4826192	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs5912437	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs7049509	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs7059257	0.94[CEU][hapmap]

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	nsv916218	chrX:79377399-80230929	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv532882	chrX:79884715-80017999	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv524776	chrX:79903169-80012807	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv33127	chrX:79989618-80370141	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv528109	chrX:79992623-80012807	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:79937000-80003600	Weak transcription	Fetal Lung	lung
2	chrX:79950400-80001600	Weak transcription	Placenta	Placenta
3	chrX:79950600-80012000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chrX:79950800-80008200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chrX:79951600-80006000	Weak transcription	Primary B cells from cord blood	blood
6	chrX:79953400-80007600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chrX:79954800-80001400	Weak transcription	Fetal Stomach	stomach
8	chrX:79954800-80022200	Weak transcription	Fetal Intestine Small	intestine
9	chrX:79960200-80020600	Weak transcription	Hela-S3	cervix
10	chrX:79965600-80034200	Weak transcription	Left Ventricle	heart
11	chrX:79966200-80001200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chrX:79968000-80001600	Weak transcription	Ovary	ovary
13	chrX:79973000-80002800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chrX:79973200-80001000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chrX:79975400-80002400	Weak transcription	Brain Angular Gyrus	brain
16	chrX:79976200-80002200	Weak transcription	GM12878-XiMat	blood
17	chrX:79978400-80001200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chrX:79979600-80001400	Weak transcription	Fetal Intestine Large	intestine
19	chrX:79979600-80003600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chrX:79979600-80022400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chrX:79980000-80002200	Weak transcription	Liver	Liver
22	chrX:79980600-80001000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chrX:79980800-80002000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chrX:79981600-80012200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chrX:79982800-80011200	Weak transcription	Pancreas	Pancrea
26	chrX:79985400-80004200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chrX:79988200-80002400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chrX:79989600-80003600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chrX:79989800-80003600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chrX:79990800-80021800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chrX:79991000-80019800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chrX:79993000-80004800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chrX:79993200-80007200	Weak transcription	NHDF-Ad	bronchial
34	chrX:79993400-80002200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chrX:79996000-80002200	Weak transcription	Adipose Nuclei	Adipose
36	chrX:79996200-80005200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chrX:79997200-80001000	Weak transcription	HSMMtube	muscle
38	chrX:79997800-80001400	Weak transcription	Thymus	Thymus
39	chrX:79998600-80000600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chrX:79998800-80000400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chrX:79998800-80001800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chrX:79999200-80000400	Strong transcription	Dnd41	blood
43	chrX:79999400-80000400	Strong transcription	Primary B cells from peripheral blood	blood
44	chrX:79999800-80001400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chrX:79999800-80001600	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chrX:79999800-80001800	Weak transcription	Duodenum Mucosa	Duodenum
47	chrX:79999800-80020600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chrX:79999800-80032000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chrX:80000000-80001600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chrX:80000000-80001600	Weak transcription	Fetal Thymus	thymus

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