Variant report

Variant	rs12508186
Chromosome Location	chr4:15548415-15548416
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	POLR2A	chr4:15548411-15548431	Gliobla	brain:	n/a	n/a

Variant related genes	Relation type
CC2D2A	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10003739	0.83[EUR][1000 genomes]
rs10008889	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs10012838	0.82[EUR][1000 genomes]
rs10020408	0.81[CEU][hapmap]
rs10022610	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs10025837	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10026851	0.83[EUR][1000 genomes]
rs10031017	0.84[EUR][1000 genomes]
rs10034328	0.83[EUR][1000 genomes]
rs1058412	1.00[CHD][hapmap]
rs10755215	1.00[CHD][hapmap]
rs10939628	0.83[EUR][1000 genomes]
rs11932730	0.94[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs11943107	0.86[EUR][1000 genomes]
rs11945626	0.82[EUR][1000 genomes]
rs12503015	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12511894	0.88[EUR][1000 genomes]
rs12640192	0.94[CEU][hapmap]
rs12645849	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs13116304	0.94[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs13121363	0.86[EUR][1000 genomes]
rs1473166	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16892140	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs16892152	0.94[CEU][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs2041671	0.94[CEU][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs2160044	0.94[CEU][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28419165	0.84[EUR][1000 genomes]
rs28522268	0.85[EUR][1000 genomes]
rs28528670	0.84[EUR][1000 genomes]
rs28534607	0.87[EUR][1000 genomes]
rs28661857	0.84[EUR][1000 genomes]
rs3822298	0.86[EUR][1000 genomes]
rs4235380	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs4279203	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4280723	0.86[EUR][1000 genomes]
rs4280724	0.86[EUR][1000 genomes]
rs4393989	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs4583752	0.94[CEU][hapmap];0.84[TSI][hapmap]
rs4591601	0.83[EUR][1000 genomes]
rs4698395	0.81[CHD][hapmap]
rs4698403	0.84[EUR][1000 genomes]
rs4698405	0.83[EUR][1000 genomes]
rs4698408	0.94[CEU][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs56041141	0.85[EUR][1000 genomes]
rs57526178	0.84[EUR][1000 genomes]
rs60040560	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs60813847	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6449149	0.86[EUR][1000 genomes]
rs6831286	0.82[EUR][1000 genomes]
rs6839438	0.83[EUR][1000 genomes]
rs73125606	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73125616	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73125627	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73125637	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73127647	0.81[EUR][1000 genomes]
rs741180	0.86[EUR][1000 genomes]
rs7661102	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs7665390	0.94[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs7665915	0.94[CEU][hapmap]
rs7675761	1.00[CHD][hapmap]
rs7682586	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs872678	0.94[CEU][hapmap];0.86[TSI][hapmap];0.84[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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12508186	CPEB2	cis	cerebellum	SCAN
rs12508186	CC2D2A	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15487400-15570400	Weak transcription	Psoas Muscle	Psoas
2	chr4:15495600-15559400	Weak transcription	HSMMtube	muscle
3	chr4:15502800-15549200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:15502800-15577600	Weak transcription	Right Ventricle	heart
5	chr4:15508200-15556400	Weak transcription	Colonic Mucosa	Colon
6	chr4:15509200-15564400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr4:15509600-15553400	Weak transcription	HepG2	liver
8	chr4:15512000-15580000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:15513000-15562400	Weak transcription	Primary B cells from cord blood	blood
10	chr4:15517800-15551600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:15517800-15593600	Weak transcription	HUVEC	blood vessel
12	chr4:15520000-15572400	Weak transcription	Small Intestine	intestine
13	chr4:15520600-15553400	Weak transcription	A549	lung
14	chr4:15526000-15558200	Weak transcription	Spleen	Spleen
15	chr4:15530200-15556600	Weak transcription	HSMM	muscle
16	chr4:15530800-15554600	Weak transcription	Placenta	Placenta
17	chr4:15530800-15554600	Weak transcription	NH-A	brain
18	chr4:15531600-15548600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:15533000-15554800	Weak transcription	Fetal Brain Male	brain
20	chr4:15537200-15565000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr4:15537400-15621000	Weak transcription	Hela-S3	cervix
22	chr4:15537800-15549000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr4:15538600-15548600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:15539000-15570400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr4:15540000-15555600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:15540200-15548800	Weak transcription	Primary T cells from cord blood	blood
27	chr4:15540200-15554400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr4:15540200-15554600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:15540200-15555400	Weak transcription	NHLF	lung
30	chr4:15540200-15556800	Weak transcription	Brain Hippocampus Middle	brain
31	chr4:15540200-15558200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr4:15540200-15558200	Weak transcription	Brain Angular Gyrus	brain
33	chr4:15540200-15558200	Weak transcription	Brain Anterior Caudate	brain
34	chr4:15540200-15559600	Weak transcription	Esophagus	oesophagus
35	chr4:15540200-15561600	Weak transcription	HMEC	breast
36	chr4:15540200-15561600	Weak transcription	NHEK	skin
37	chr4:15540200-15562600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr4:15540400-15549200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr4:15540400-15551600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr4:15540400-15554600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr4:15540400-15563200	Weak transcription	Brain Substantia Nigra	brain
42	chr4:15540400-15565000	Weak transcription	NHDF-Ad	bronchial
43	chr4:15541600-15554600	Weak transcription	Osteobl	bone
44	chr4:15542000-15548600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:15542600-15554200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:15543800-15550000	Strong transcription	Colon Smooth Muscle	Colon
47	chr4:15543800-15570600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr4:15544000-15553800	Weak transcription	Fetal Kidney	kidney
49	chr4:15544400-15553400	Weak transcription	Fetal Intestine Large	intestine
50	chr4:15544400-15562400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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