Variant report

Variant	rs9377004
Chromosome Location	chr6:146873614-146873615
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11155475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189826	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804286	0.95[CEU][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3804288	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs3804289	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs6570768	0.95[CEU][hapmap]
rs6915731	0.95[CEU][hapmap]
rs6918907	0.81[EUR][1000 genomes]
rs6939108	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs7773384	0.92[EUR][1000 genomes]
rs9373498	0.94[EUR][1000 genomes]
rs9377003	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9390393	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399580	0.89[EUR][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	nsv1033913	chr6:146572989-147092365	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv538466	chr6:146572989-147092365	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv886749	chr6:146679735-147123699	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9377004	STX11	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146865800-146877400	Weak transcription	Placenta	Placenta
2	chr6:146865800-146878200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr6:146866400-146881800	Weak transcription	Brain Germinal Matrix	brain
4	chr6:146866600-146875800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:146866600-146876200	Weak transcription	Psoas Muscle	Psoas
6	chr6:146866600-146877800	Weak transcription	Gastric	stomach
7	chr6:146866600-146877800	Weak transcription	Lung	lung
8	chr6:146866600-146883800	Weak transcription	Small Intestine	intestine
9	chr6:146866600-146885800	Weak transcription	Pancreas	Pancrea
10	chr6:146866800-146877600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:146866800-146878000	Weak transcription	Brain Substantia Nigra	brain
12	chr6:146867000-146876000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr6:146867000-146877200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:146867000-146877800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:146867000-146880600	Weak transcription	Right Ventricle	heart
16	chr6:146867200-146875600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:146867200-146875600	Weak transcription	Colonic Mucosa	Colon
18	chr6:146867200-146877800	Weak transcription	Primary T cells from cord blood	blood
19	chr6:146867400-146875400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:146867400-146875800	Weak transcription	Brain Hippocampus Middle	brain
21	chr6:146867400-146877400	Weak transcription	Fetal Intestine Small	intestine
22	chr6:146867800-146875200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr6:146868000-146873800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:146868200-146876800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:146868400-146875200	Weak transcription	Right Atrium	heart
26	chr6:146868400-146875600	Weak transcription	HSMMtube	muscle
27	chr6:146868400-146876000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:146868600-146875800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr6:146868800-146875600	Weak transcription	Hela-S3	cervix
30	chr6:146869600-146873800	Strong transcription	Osteobl	bone
31	chr6:146869600-146877000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:146870000-146875800	Weak transcription	Colon Smooth Muscle	Colon
33	chr6:146870000-146876800	Strong transcription	HepG2	liver
34	chr6:146870000-146877000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:146870000-146877000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:146870200-146877000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:146870400-146874000	Strong transcription	HUVEC	blood vessel
38	chr6:146870600-146877000	Strong transcription	HSMM	muscle
39	chr6:146870800-146876800	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr6:146870800-146876800	Strong transcription	NH-A	brain
41	chr6:146870800-146877000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:146871000-146874400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr6:146871000-146875600	Weak transcription	Spleen	Spleen
44	chr6:146871000-146877200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr6:146871200-146875800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr6:146871400-146875600	Weak transcription	Fetal Intestine Large	intestine
47	chr6:146871400-146876000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr6:146871600-146875200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr6:146871800-146875600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:146871800-146876000	Weak transcription	HMEC	breast

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