Variant report

Variant	rs9462209
Chromosome Location	chr6:36628042-36628043
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36618015..36619715-chr6:36627253..36629685,2	MCF-7	breast:
2	chr6:36626473..36628728-chr6:36691772..36694267,2	MCF-7	breast:
3	chr6:36560914..36563599-chr6:36627068..36629393,2	K562	blood:
4	chr6:36627657..36630518-chr6:36646219..36647988,2	K562	blood:

Variant related genes	Relation type
ENSG00000124762	Chromatin interaction
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11969445	0.92[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];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4568449	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6457933	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6907437	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6907793	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6930671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6936598	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6936993	1.00[ASW][hapmap];0.96[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];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7740181	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9462208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470362	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9470363	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv3448277	chr6:36625374-36628672	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9462209	MDGA1	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36611600-36628600	Weak transcription	Right Atrium	heart
2	chr6:36619400-36628400	Weak transcription	Adipose Nuclei	Adipose
3	chr6:36620200-36628600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:36622200-36628600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr6:36622400-36628800	Enhancers	GM12878-XiMat	blood
6	chr6:36623200-36628600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:36623400-36628800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:36624600-36628800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:36625000-36628200	Enhancers	Colon Smooth Muscle	Colon
10	chr6:36625000-36628800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:36625600-36628400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:36625600-36628800	Enhancers	NHDF-Ad	bronchial
13	chr6:36625800-36628400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:36626000-36628200	Enhancers	Fetal Heart	heart
15	chr6:36626200-36628200	Weak transcription	Fetal Intestine Large	intestine
16	chr6:36626200-36629600	Weak transcription	Hela-S3	cervix
17	chr6:36626400-36628600	Weak transcription	NH-A	brain
18	chr6:36626800-36628400	Bivalent Enhancer	Fetal Muscle Leg	muscle
19	chr6:36627200-36628400	Enhancers	Ovary	ovary
20	chr6:36627400-36628200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
21	chr6:36627400-36628600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:36627400-36628800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr6:36627400-36629800	Bivalent Enhancer	Fetal Thymus	thymus
24	chr6:36627600-36628400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:36627600-36628400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr6:36627600-36628400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr6:36627600-36628400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr6:36627600-36628400	Weak transcription	Left Ventricle	heart
29	chr6:36627600-36628600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:36627600-36628600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:36627600-36628600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:36627600-36628600	Weak transcription	Esophagus	oesophagus
33	chr6:36627600-36628800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:36627600-36628800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:36627800-36628400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:36627800-36634000	Weak transcription	HMEC	breast
37	chr6:36627800-36634000	Weak transcription	HSMM	muscle
38	chr6:36628000-36628200	Flanking Active TSS	Placenta	Placenta
39	chr6:36628000-36628200	Bivalent Enhancer	K562	blood
40	chr6:36628000-36628400	Enhancers	Colonic Mucosa	Colon
41	chr6:36628000-36628600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:36628000-36628600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
43	chr6:36628000-36629000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
44	chr6:36628000-36629000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:36628000-36629000	Flanking Active TSS	Fetal Intestine Small	intestine
46	chr6:36628000-36631200	Enhancers	Primary B cells from cord blood	blood

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