Variant report

Variant	rs12202537
Chromosome Location	chr6:144796516-144796517
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:144795886..144798069-chr6:144800521..144802529,2	K562	blood:
2	chr6:144793191..144795370-chr6:144795376..144798079,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10447422	0.86[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap]
rs10457764	0.86[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs10499230	0.86[CEU][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap]
rs12200263	0.86[CEU][hapmap]
rs12202539	0.86[CEU][hapmap]
rs12204734	0.95[GIH][hapmap];0.94[TSI][hapmap]
rs12209699	0.95[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs12209889	0.86[CEU][hapmap]
rs1918749	0.95[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs28588721	0.86[EUR][1000 genomes]
rs34983431	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4259269	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4584002	0.91[GIH][hapmap]
rs4896724	0.95[GIH][hapmap]
rs6570634	0.93[GIH][hapmap];0.81[TSI][hapmap]
rs6908911	0.95[GIH][hapmap]
rs6912724	0.90[GIH][hapmap]
rs6917268	0.93[CEU][hapmap]
rs6917519	0.93[CEU][hapmap]
rs73780588	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7773603	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs9321977	0.90[GIH][hapmap]
rs9496982	0.93[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1023014	chr6:144717963-144806691	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv886739	chr6:144719765-144796516	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1015228	chr6:144780458-144989321	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv538462	chr6:144780458-144989321	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12202537	MRPS27	trans	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144741000-144801800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:144756000-144810600	Weak transcription	Small Intestine	intestine
3	chr6:144763000-144813800	Weak transcription	Brain Anterior Caudate	brain
4	chr6:144764400-144838800	Weak transcription	A549	lung
5	chr6:144771400-144815800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:144771800-144811800	Weak transcription	Stomach Mucosa	stomach
7	chr6:144778600-144813800	Weak transcription	Hela-S3	cervix
8	chr6:144781000-144801000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:144781800-144806600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:144782000-144799600	Weak transcription	Psoas Muscle	Psoas
11	chr6:144782000-144806600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:144782000-144806600	Weak transcription	Brain Substantia Nigra	brain
13	chr6:144782000-144806600	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:144782000-144806600	Weak transcription	Spleen	Spleen
15	chr6:144782000-144809800	Weak transcription	Gastric	stomach
16	chr6:144782200-144806600	Weak transcription	Colonic Mucosa	Colon
17	chr6:144782400-144801200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:144782800-144801000	Weak transcription	NH-A	brain
19	chr6:144783400-144798800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr6:144783800-144802800	Weak transcription	NHLF	lung
21	chr6:144784600-144812000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:144785000-144801000	Weak transcription	Right Ventricle	heart
23	chr6:144788600-144797200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:144788600-144806400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:144788600-144808800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:144788800-144796800	Weak transcription	Fetal Stomach	stomach
27	chr6:144788800-144798200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:144788800-144799600	Weak transcription	Pancreas	Pancrea
29	chr6:144788800-144801000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:144788800-144801000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:144788800-144812000	Weak transcription	Esophagus	oesophagus
32	chr6:144788800-144821600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr6:144789400-144822800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr6:144789600-144812200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:144790400-144802800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:144790600-144798600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr6:144790800-144798600	Weak transcription	Fetal Heart	heart
38	chr6:144792000-144810000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:144792200-144796800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:144792200-144796800	Weak transcription	Fetal Intestine Small	intestine
41	chr6:144792200-144798000	Strong transcription	Primary T cells from cord blood	blood
42	chr6:144792200-144804400	Strong transcription	Fetal Thymus	thymus
43	chr6:144792400-144797800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
44	chr6:144792400-144800000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr6:144792400-144802600	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr6:144792400-144815400	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr6:144792400-144823800	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr6:144792400-144824400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr6:144792400-144826000	Strong transcription	Primary B cells from peripheral blood	blood
50	chr6:144792600-144797200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links