Variant report

Variant	rs9467478
Chromosome Location	chr6:25370970-25370971
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs16890520	1.00[JPT][hapmap]
rs16890548	1.00[JPT][hapmap]
rs16890551	1.00[JPT][hapmap]
rs1927695	0.93[CEU][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55731467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57992726	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58095699	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58924292	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60556647	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73730705	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7769124	1.00[JPT][hapmap]
rs9461146	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467476	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9467480	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467481	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][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	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv601168	chr6:25346334-25393306	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9467478	PRSS16	cis	cerebellum	SCAN
rs9467478	BTN3A2	cis	parietal	SCAN
rs9467478	HIST1H2BE	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25366600-25371800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr6:25367800-25371000	Enhancers	Primary hematopoietic stem cells	blood
3	chr6:25368000-25378400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:25368200-25371600	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr6:25368200-25375400	Weak transcription	Primary B cells from cord blood	blood
6	chr6:25369200-25371400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr6:25369200-25371600	Enhancers	Fetal Intestine Small	intestine
8	chr6:25369400-25371000	Enhancers	Pancreas	Pancrea
9	chr6:25369400-25371000	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr6:25369400-25371000	Enhancers	Stomach Mucosa	stomach
11	chr6:25369400-25371400	Enhancers	Fetal Intestine Large	intestine
12	chr6:25369400-25371600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:25369600-25371000	Flanking Active TSS	GM12878-XiMat	blood
14	chr6:25369600-25371200	Enhancers	Small Intestine	intestine
15	chr6:25369800-25371200	Enhancers	Primary B cells from peripheral blood	blood
16	chr6:25370000-25371200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr6:25370200-25371000	Enhancers	Aorta	Aorta
18	chr6:25370200-25371000	Enhancers	HSMMtube	muscle
19	chr6:25370400-25371000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:25370400-25371200	Enhancers	Fetal Thymus	thymus
21	chr6:25370400-25371400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:25370400-25371600	Enhancers	Primary T cells from cord blood	blood
23	chr6:25370400-25371800	Enhancers	Thymus	Thymus
24	chr6:25370400-25374000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:25370400-25377200	Weak transcription	Right Atrium	heart
26	chr6:25370400-25378400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:25370600-25371000	Enhancers	Fetal Brain Female	brain
28	chr6:25370600-25371600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:25370600-25372000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr6:25370800-25371200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:25370800-25371200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr6:25370800-25371200	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr6:25370800-25371200	Enhancers	Brain Germinal Matrix	brain
34	chr6:25370800-25371400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:25370800-25371400	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr6:25370800-25371600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr6:25370800-25371600	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr6:25370800-25371800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr6:25370800-25371800	Enhancers	Duodenum Mucosa	Duodenum
40	chr6:25370800-25372200	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr6:25370800-25377200	Weak transcription	Gastric	stomach
42	chr6:25370800-25388800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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