Variant report

Variant	rs9473086
Chromosome Location	chr6:12957035-12957036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10948372	0.90[EUR][1000 genomes]
rs11755663	1.00[JPT][hapmap]
rs11755825	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs11756003	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526453	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12528956	1.00[CHD][hapmap]
rs12530250	1.00[JPT][hapmap]
rs13194360	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs13201878	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13219256	1.00[CHD][hapmap]
rs13220463	1.00[JPT][hapmap]
rs1332841	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1332845	1.00[CHD][hapmap]
rs1332847	1.00[CHD][hapmap]
rs1360579	1.00[JPT][hapmap]
rs1537340	1.00[CHD][hapmap]
rs17679501	1.00[JPT][hapmap]
rs2183072	1.00[JPT][hapmap]
rs2327621	1.00[CHD][hapmap]
rs34175679	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35266083	0.91[EUR][1000 genomes]
rs36049381	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4131857	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs4236093	0.81[CEU][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes]
rs4331981	1.00[JPT][hapmap]
rs4588689	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711857	1.00[JPT][hapmap]
rs4711858	1.00[JPT][hapmap]
rs4714946	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs62386820	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62386821	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458503	1.00[CHD][hapmap]
rs66820937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906017	0.90[EUR][1000 genomes]
rs6906890	0.81[CEU][hapmap];0.81[TSI][hapmap];0.91[EUR][1000 genomes]
rs6907388	1.00[JPT][hapmap]
rs6929107	0.88[EUR][1000 genomes]
rs7739181	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7775710	0.81[CEU][hapmap];0.90[EUR][1000 genomes]
rs7775901	1.00[JPT][hapmap]
rs9296494	1.00[CHD][hapmap]
rs9472777	1.00[JPT][hapmap]
rs9472786	1.00[CHD][hapmap];1.00[JPT][hapmap]

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	esv3521000	chr6:12561306-13128519	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3521001	chr6:12561306-13128519	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv830588	chr6:12793530-12972493	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv5202	chr6:12916229-12958517	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv817350	chr6:12922859-13137655	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9473086	HIVEP1	cis	parietal	SCAN
rs9473086	RANBP9	cis	lymphoblastoid	seeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12952000-12957400	Weak transcription	Left Ventricle	heart
2	chr6:12953000-12957400	Weak transcription	Brain Angular Gyrus	brain
3	chr6:12953000-12957400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:12953200-12957400	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:12953400-12957400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr6:12955600-12957400	Enhancers	Fetal Heart	heart
7	chr6:12955800-12958800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:12956000-12957200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
9	chr6:12956200-12957200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
10	chr6:12956200-12957400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:12956400-12957200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
12	chr6:12956400-12957200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
13	chr6:12956400-12957200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
14	chr6:12956400-12957200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:12956400-12957800	Active TSS	Primary hematopoietic stem cells	blood
16	chr6:12956600-12957200	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:12956600-12957200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:12956600-12957200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr6:12956600-12957400	Enhancers	Brain Germinal Matrix	brain
20	chr6:12956600-12957400	Enhancers	Brain Substantia Nigra	brain
21	chr6:12956600-12957400	Active TSS	Fetal Brain Male	brain
22	chr6:12956600-12957400	Enhancers	Fetal Brain Female	brain
23	chr6:12956600-12958400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr6:12956600-12958400	Active TSS	Primary T cells from cord blood	blood
25	chr6:12956800-12957200	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
26	chr6:12956800-12957200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr6:12956800-12957200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr6:12956800-12957200	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr6:12956800-12957400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:12956800-12957400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
31	chr6:12956800-12957400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
32	chr6:12956800-12957400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:12956800-12957400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
34	chr6:12956800-12957400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:12956800-12957400	Enhancers	Right Ventricle	heart
36	chr6:12956800-12957600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:12956800-12958000	Active TSS	Primary B cells from cord blood	blood
38	chr6:12956800-12959400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:12957000-12957200	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
40	chr6:12957000-12957200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
41	chr6:12957000-12957200	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:12957000-12957200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:12957000-12957200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:12957000-12957200	Flanking Active TSS	Brain Anterior Caudate	brain
45	chr6:12957000-12957200	Flanking Active TSS	Brain Cingulate Gyrus	brain
46	chr6:12957000-12957200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr6:12957000-12957200	Enhancers	Fetal Lung	lung
48	chr6:12957000-12957200	Flanking Active TSS	Fetal Thymus	thymus
49	chr6:12957000-12957200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
50	chr6:12957000-12957200	Flanking Active TSS	Thymus	Thymus

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