Variant report

Variant	rs9380586
Chromosome Location	chr6:36631564-36631565
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36631478..36636279-chr6:36645838..36648638,4	K562	blood:
2	chr6:36592740..36594908-chr6:36630647..36632987,2	MCF-7	breast:
3	chr6:36561045..36564139-chr6:36628780..36632621,3	K562	blood:
4	chr6:36628763..36632041-chr6:36634655..36636899,4	MCF-7	breast:
5	chr6:36630192..36637203-chr6:36642841..36649451,13	K562	blood:
6	chr6:36628825..36632720-chr6:36633397..36637228,8	MCF-7	breast:
7	chr6:36623725..36625807-chr6:36629087..36632013,3	K562	blood:

Variant related genes	Relation type
ENSG00000124762	Chromatin interaction
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1321312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969701	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1977172	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3176330	0.92[ASN][1000 genomes]
rs3176331	0.89[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs3829966	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3829967	0.93[ASN][1000 genomes]
rs3829968	0.90[ASN][1000 genomes]
rs4135234	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4135237	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4135239	0.93[ASN][1000 genomes]
rs4713997	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]
rs4714000	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6457936	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6902994	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6907801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7452626	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs762623	0.89[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs9380585	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]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9380586	MXRA7	trans	lymphoblastoid	seeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36627800-36634000	Weak transcription	HMEC	breast
2	chr6:36627800-36634000	Weak transcription	HSMM	muscle
3	chr6:36628200-36636600	Enhancers	Primary B cells from peripheral blood	blood
4	chr6:36629000-36633600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr6:36629000-36633800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:36629200-36633400	Weak transcription	Ovary	ovary
7	chr6:36629200-36634200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:36629200-36634200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:36629200-36634600	Weak transcription	Liver	Liver
10	chr6:36629200-36634800	Weak transcription	Right Atrium	heart
11	chr6:36629200-36635000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:36629200-36635000	Weak transcription	Right Ventricle	heart
13	chr6:36629400-36634600	Weak transcription	Adipose Nuclei	Adipose
14	chr6:36629600-36631600	Weak transcription	K562	blood
15	chr6:36629800-36631800	Enhancers	Fetal Thymus	thymus
16	chr6:36630000-36631800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr6:36630200-36631800	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr6:36630600-36631800	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr6:36630800-36634200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr6:36630800-36634200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:36630800-36635000	Weak transcription	Fetal Heart	heart
22	chr6:36631000-36631800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:36631000-36632000	Enhancers	Duodenum Mucosa	Duodenum
24	chr6:36631000-36632600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:36631000-36632600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:36631000-36634000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:36631000-36634200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:36631000-36634200	Weak transcription	Colonic Mucosa	Colon
29	chr6:36631000-36644000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:36631200-36631600	Enhancers	GM12878-XiMat	blood
31	chr6:36631200-36631600	Enhancers	Hela-S3	cervix
32	chr6:36631200-36632200	Enhancers	HepG2	liver
33	chr6:36631200-36632400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr6:36631200-36633600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:36631200-36634000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:36631200-36634000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:36631200-36634000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr6:36631200-36634000	Weak transcription	Pancreas	Pancrea
39	chr6:36631200-36634000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr6:36631200-36634200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:36631200-36634200	Weak transcription	Esophagus	oesophagus
42	chr6:36631400-36633800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr6:36631400-36633800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:36631400-36633800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:36631400-36634000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:36631400-36634000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:36631400-36634000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:36631400-36634000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:36631400-36634000	Weak transcription	Fetal Intestine Large	intestine
50	chr6:36631400-36634000	Weak transcription	NHEK	skin

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