Variant report

Variant	rs12199291
Chromosome Location	chr6:166883844-166883845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr6:166883741-166883941	MCF10A-Er-Src	breast:	n/a	chr6:166883834-166883843 chr6:166883833-166883842 chr6:166883831-166883845 chr6:166883828-166883848
2	USF2	chr6:166883756-166883881	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr6:166883110-166884808	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:166754479..166756533-chr6:166881640..166884124,2	MCF-7	breast:

Variant related genes	Relation type
RPS6KA2-IT1	TF binding region
ENSG00000198818	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12202788	0.81[CHD][hapmap];0.83[GIH][hapmap];0.81[MEX][hapmap]
rs2235284	0.86[CEU][hapmap]
rs2281046	0.93[CEU][hapmap];0.80[TSI][hapmap]
rs9295349	0.89[CHD][hapmap];0.81[MEX][hapmap]

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	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886937	chr6:166830696-166922813	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv886938	chr6:166859725-166904398	Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv886939	chr6:166859725-166922813	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv886940	chr6:166881023-166895934	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12199291	PARK2	cis	cerebellum	SCAN
rs12199291	NCOR1	trans	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166808200-166911800	Weak transcription	Psoas Muscle	Psoas
2	chr6:166824000-166901400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:166862400-166900600	Weak transcription	Primary T cells from cord blood	blood
4	chr6:166862400-166920600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:166863600-166900200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:166863600-166902000	Weak transcription	Small Intestine	intestine
7	chr6:166864800-166899800	Weak transcription	Esophagus	oesophagus
8	chr6:166867400-166892800	Weak transcription	Fetal Brain Male	brain
9	chr6:166867600-166900000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:166870400-166898400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:166871000-166901400	Weak transcription	Stomach Mucosa	stomach
12	chr6:166872000-166900400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:166872200-166900400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr6:166873000-166902800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:166874200-166885200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:166874800-166903000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr6:166875000-166900800	Weak transcription	Fetal Heart	heart
18	chr6:166875400-166885400	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr6:166875600-166884200	Strong transcription	Gastric	stomach
20	chr6:166875800-166887000	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr6:166875800-166894000	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr6:166876000-166885000	Strong transcription	Right Ventricle	heart
23	chr6:166876000-166888800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:166876000-166901400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:166876200-166886600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:166877000-166885200	Strong transcription	Spleen	Spleen
27	chr6:166877200-166904400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr6:166877200-166908800	Weak transcription	Colonic Mucosa	Colon
29	chr6:166877600-166885200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:166878200-166902000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr6:166879000-166900600	Weak transcription	Primary B cells from cord blood	blood
32	chr6:166879800-166891400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:166880200-166887800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:166880200-166888400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:166880200-166890600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr6:166880200-166892200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:166880200-166900000	Weak transcription	Fetal Intestine Large	intestine
38	chr6:166880400-166887600	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr6:166880400-166887600	Weak transcription	HSMMtube	muscle
40	chr6:166880400-166887800	Weak transcription	HSMM	muscle
41	chr6:166880400-166900000	Weak transcription	Fetal Lung	lung
42	chr6:166880600-166884000	Strong transcription	Fetal Muscle Leg	muscle
43	chr6:166880600-166885600	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr6:166880600-166887000	Strong transcription	Fetal Stomach	stomach
45	chr6:166880600-166895800	Weak transcription	NHDF-Ad	bronchial
46	chr6:166880600-166899800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr6:166880800-166884200	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr6:166880800-166893600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:166880800-166904400	Weak transcription	NH-A	brain
50	chr6:166881000-166887000	Strong transcription	Left Ventricle	heart

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