Variant report

Variant	rs2236382
Chromosome Location	chr6:133138749-133138750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:133054032..133057251-chr6:133136548..133139421,3	K562	blood:
2	chr19:12885475..12887158-chr6:133138358..133141147,2	K562	blood:
3	chr17:40214097..40215598-chr6:133136759..133139699,2	K562	blood:
4	chr6:132855902..132859597-chr6:133135974..133139810,3	K562	blood:
5	chr6:133118544..133124606-chr6:133132137..133138834,13	MCF-7	breast:
6	chr6:133117688..133126502-chr6:133133829..133139054,19	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146409	Chromatin interaction
ENSG00000237110	Chromatin interaction
ENSG00000095066	Chromatin interaction
ENSG00000093134	Chromatin interaction
ENSG00000187595	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11154696	0.91[MEX][hapmap]
rs1124450	0.86[CHD][hapmap]
rs12200907	0.88[CHD][hapmap]
rs12202302	0.85[CHB][hapmap];0.83[CHD][hapmap];0.88[MEX][hapmap]
rs1359142	0.88[CHD][hapmap]
rs1408062	0.89[CHD][hapmap]
rs2236381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4599669	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4897617	0.88[CHD][hapmap]
rs6926466	0.85[CHB][hapmap];0.83[CHD][hapmap];0.88[MEX][hapmap]
rs761125	0.85[CHB][hapmap]
rs7751879	0.86[CEU][hapmap];0.85[CHB][hapmap]
rs7756588	0.89[CHD][hapmap]
rs7764152	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs9321374	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9373030	0.89[CHD][hapmap]
rs9389034	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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]
rs9399043	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9399044	0.95[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap]
rs9493450	0.83[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap]
rs9493451	0.90[CHB][hapmap]
rs9493458	0.86[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][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	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1015742	chr6:132933666-133285852	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv886676	chr6:133111706-133168582	Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	esv1806734	chr6:133125643-133168582	Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2236382	HBII-429	cis	multi-tissue	Pritchard
rs2236382	SNORA33	cis	cerebellum	SCAN
rs2236382	ACA33	cis	multi-tissue	Pritchard
rs2236382	C6orf192	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133136000-133139000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
2	chr6:133136000-133139200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
3	chr6:133136000-133139200	Transcr. at gene 5' and 3'	K562	blood
4	chr6:133136000-133139800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:133136200-133139000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:133136200-133139000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
7	chr6:133136200-133139400	Transcr. at gene 5' and 3'	A549	lung
8	chr6:133136200-133140600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
9	chr6:133136600-133139000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:133137000-133139200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:133137200-133145400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr6:133137400-133138800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:133137400-133139600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:133137400-133141000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr6:133137400-133141000	Strong transcription	Aorta	Aorta
16	chr6:133137400-133141200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
17	chr6:133137400-133141400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr6:133137600-133138800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr6:133137600-133138800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:133137600-133138800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr6:133137600-133139000	Genic enhancers	Fetal Heart	heart
22	chr6:133137600-133139600	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr6:133137600-133140000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
24	chr6:133137600-133141200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr6:133137800-133138800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:133137800-133138800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr6:133137800-133138800	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr6:133137800-133138800	Weak transcription	Lung	lung
29	chr6:133137800-133139600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:133137800-133139600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr6:133137800-133139600	Strong transcription	Esophagus	oesophagus
32	chr6:133137800-133139600	Genic enhancers	HSMM	muscle
33	chr6:133137800-133140200	Genic enhancers	Primary T cells fromperipheralblood	blood
34	chr6:133137800-133140600	Strong transcription	Pancreas	Pancrea
35	chr6:133137800-133140800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr6:133137800-133141000	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr6:133137800-133141200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr6:133137800-133141200	Strong transcription	Placenta	Placenta
39	chr6:133137800-133141400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:133137800-133141400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr6:133137800-133141600	Strong transcription	Fetal Thymus	thymus
42	chr6:133137800-133142200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:133137800-133142400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr6:133137800-133142400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr6:133137800-133143600	Weak transcription	Right Atrium	heart
46	chr6:133138000-133138800	Weak transcription	Fetal Intestine Small	intestine
47	chr6:133138000-133138800	Weak transcription	Gastric	stomach
48	chr6:133138000-133138800	Genic enhancers	Rectal Smooth Muscle	rectum
49	chr6:133138000-133139000	Strong transcription	Psoas Muscle	Psoas
50	chr6:133138000-133139000	Strong transcription	Right Ventricle	heart

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