Variant report

Variant	rs12191476
Chromosome Location	chr6:38223386-38223387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38221614..38223859-chr6:38225623..38227159,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1076704	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10947721	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10947722	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10947723	0.92[LWK][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs12190288	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12194178	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12214213	1.00[JPT][hapmap];0.82[LWK][hapmap];0.86[YRI][hapmap]
rs12215707	1.00[JPT][hapmap];0.86[YRI][hapmap]
rs13206817	0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.86[YRI][hapmap]
rs17685625	1.00[ASW][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1885322	0.82[LWK][hapmap]
rs1885323	0.93[JPT][hapmap]
rs2092425	0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.86[YRI][hapmap]
rs34366378	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34919903	0.83[EUR][1000 genomes]
rs4626419	0.85[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs62397019	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs73730921	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9470839	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12191476	MOCS1	cis	parietal	SCAN
rs12191476	TCP11	cis	parietal	SCAN
rs12191476	TMEM217	cis	cerebellum	SCAN
rs12191476	RNF8	cis	parietal	SCAN
rs12191476	SLC26A8	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38181400-38229400	Weak transcription	Fetal Intestine Small	intestine
2	chr6:38194400-38230200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:38204800-38229400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:38205200-38228800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr6:38207800-38229400	Weak transcription	Brain Hippocampus Middle	brain
6	chr6:38208000-38226400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr6:38208200-38226000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:38208200-38227600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:38208200-38236600	Weak transcription	Gastric	stomach
10	chr6:38208200-38255000	Weak transcription	Ovary	ovary
11	chr6:38209000-38229000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:38209200-38227000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:38213400-38228800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:38213400-38232400	Weak transcription	Right Ventricle	heart
15	chr6:38215200-38229400	Weak transcription	Brain Angular Gyrus	brain
16	chr6:38215600-38229000	Weak transcription	Brain Substantia Nigra	brain
17	chr6:38216000-38229000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:38216000-38238000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr6:38216800-38227000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr6:38217000-38227000	Weak transcription	NHDF-Ad	bronchial
21	chr6:38217200-38226200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:38218000-38229600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:38218000-38229800	Weak transcription	Spleen	Spleen
24	chr6:38218800-38232200	Weak transcription	Small Intestine	intestine
25	chr6:38219200-38227200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:38219400-38229600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:38220000-38238200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:38220200-38225600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:38220200-38229400	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:38220400-38223400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:38220400-38225600	Weak transcription	Placenta	Placenta
32	chr6:38220400-38226800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:38220400-38226800	Weak transcription	Thymus	Thymus
34	chr6:38220400-38229400	Weak transcription	Brain Anterior Caudate	brain
35	chr6:38220600-38228800	Weak transcription	HSMMtube	muscle
36	chr6:38220600-38241600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr6:38220800-38226600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:38221000-38223400	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr6:38221000-38223800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:38221000-38224600	Strong transcription	Primary B cells from cord blood	blood
41	chr6:38221200-38223600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:38221200-38224400	Strong transcription	Primary T cells from cord blood	blood
43	chr6:38221200-38224400	Strong transcription	Adipose Nuclei	Adipose
44	chr6:38221200-38225200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr6:38221600-38223800	Strong transcription	Fetal Lung	lung
46	chr6:38221600-38224600	Strong transcription	Duodenum Mucosa	Duodenum
47	chr6:38221600-38224600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr6:38221600-38224800	Strong transcription	Fetal Stomach	stomach
49	chr6:38221600-38226400	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr6:38221800-38226600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links