Variant report

Variant	rs7527272
Chromosome Location	chr1:97737237-97737238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10157665	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10465749	0.84[EUR][1000 genomes]
rs11589238	0.95[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs12029106	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12030332	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12044501	0.87[AFR][1000 genomes]
rs12046744	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12049622	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1520668	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2049112	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28755414	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4264037	0.95[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56300389	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59114215	0.87[AFR][1000 genomes]
rs61786278	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61786354	0.86[EUR][1000 genomes]
rs6700670	0.90[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs72726670	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72726689	0.86[EUR][1000 genomes]
rs74104326	0.80[AFR][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	nsv491816	chr1:97266403-98223619	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv530048	chr1:97457175-98031501	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007950	chr1:97466488-98021146	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv533039	chr1:97665736-98343102	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv470728	chr1:97703325-97761972	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7527272	SASS6	cis	cerebellum	SCAN
rs7527272	MTF2	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97720600-97772000	Weak transcription	Ovary	ovary
2	chr1:97724000-97773200	Weak transcription	Lung	lung
3	chr1:97724400-97740200	Weak transcription	Primary T cells from cord blood	blood
4	chr1:97730400-97769800	Weak transcription	Primary B cells from cord blood	blood
5	chr1:97731400-97761200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr1:97731600-97757600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:97731600-97757800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:97733400-97748800	Weak transcription	Dnd41	blood
9	chr1:97733600-97742400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:97733600-97742600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:97733600-97769800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:97733800-97739000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr1:97733800-97740200	Weak transcription	Psoas Muscle	Psoas
14	chr1:97734400-97737800	Weak transcription	Liver	Liver
15	chr1:97735800-97739800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr1:97736400-97738000	Enhancers	NH-A	brain
17	chr1:97736400-97738200	Enhancers	A549	lung
18	chr1:97736600-97737800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:97736600-97737800	Enhancers	Small Intestine	intestine
20	chr1:97736600-97738000	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr1:97736600-97738000	Enhancers	Adipose Nuclei	Adipose
22	chr1:97736600-97738200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:97736600-97738400	Enhancers	Stomach Mucosa	stomach
24	chr1:97736800-97738400	Enhancers	Fetal Lung	lung
25	chr1:97736800-97741600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:97736800-97747600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:97736800-97771600	Weak transcription	Left Ventricle	heart
28	chr1:97737000-97738600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:97737000-97740600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:97737200-97737600	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr1:97737200-97737800	Enhancers	HepG2	liver
32	chr1:97737200-97738000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:97737200-97738000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr1:97737200-97738000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:97737200-97738000	Enhancers	Muscle Satellite Cultured Cells	--
36	chr1:97737200-97738000	Enhancers	Hela-S3	cervix
37	chr1:97737200-97738400	Enhancers	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links