Variant report

Variant	rs9470706
Chromosome Location	chr6:37761961-37761962
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37760526..37762581-chr6:37765798..37767816,2	MCF-7	breast:
2	chr6:37759642..37762006-chr6:37820086..37822847,3	MCF-7	breast:
3	chr6:37756505..37762867-chr6:37772774..37778127,6	MCF-7	breast:
4	chr6:37761178..37763195-chr6:37774802..37776873,2	MCF-7	breast:
5	chr6:37742631..37746387-chr6:37760505..37763552,3	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10456096	0.88[CHB][hapmap]
rs10485029	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10947707	0.85[EUR][1000 genomes]
rs1187421	0.85[CEU][hapmap];0.89[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs12190570	0.92[CEU][hapmap];0.89[CHB][hapmap];0.87[EUR][1000 genomes]
rs2055206	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs259679	0.92[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs259718	0.92[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs2645117	0.89[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap]
rs2645124	0.92[CEU][hapmap];0.86[CHB][hapmap]
rs34592529	0.87[EUR][1000 genomes]
rs35806631	0.88[EUR][1000 genomes]
rs35925070	0.85[EUR][1000 genomes]
rs4711514	0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs6458029	0.88[CHB][hapmap]
rs9296232	0.88[CHB][hapmap];1.00[CHD][hapmap]
rs9394460	0.88[CHB][hapmap];1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9470706	MDGA1	cis	cerebellum	SCAN
rs9470706	KCNK17	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37758600-37762600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr6:37759200-37762400	Weak transcription	HSMMtube	muscle
3	chr6:37759200-37768400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:37759600-37762400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:37759600-37766000	Weak transcription	Lung	lung
6	chr6:37759600-37767200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:37759600-37767200	Weak transcription	Right Atrium	heart
8	chr6:37759800-37762400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:37759800-37762400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:37759800-37762400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr6:37759800-37762400	Weak transcription	Psoas Muscle	Psoas
12	chr6:37759800-37762400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:37759800-37762400	Weak transcription	HSMM	muscle
14	chr6:37759800-37762400	Weak transcription	NHEK	skin
15	chr6:37759800-37762600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:37759800-37762600	Weak transcription	HMEC	breast
17	chr6:37759800-37762600	Weak transcription	NH-A	brain
18	chr6:37759800-37763800	Weak transcription	Liver	Liver
19	chr6:37759800-37764000	Weak transcription	Pancreas	Pancrea
20	chr6:37759800-37764200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:37759800-37768600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr6:37760000-37762600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:37761000-37762400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:37761000-37762400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:37761000-37762600	Weak transcription	NHLF	lung
26	chr6:37761000-37764200	Weak transcription	Fetal Muscle Leg	muscle
27	chr6:37761200-37762400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:37761400-37762400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:37761400-37762400	Weak transcription	HepG2	liver
30	chr6:37761400-37762400	Weak transcription	NHDF-Ad	bronchial
31	chr6:37761400-37762400	Weak transcription	Osteobl	bone
32	chr6:37761600-37762000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:37761600-37766200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links