Variant report

Variant	rs17312996
Chromosome Location	chr3:134094894-134094895
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:134091805..134100491-chr3:134198620..134206897,15	MCF-7	breast:
2	chr3:134024307..134037207-chr3:134080573..134100993,88	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182923	Chromatin interaction
ENSG00000129055	Chromatin interaction
ENSG00000240006	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10935116	1.00[CHB][hapmap]
rs11707704	1.00[ASN][1000 genomes]
rs11917363	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11919447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11923513	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928672	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11928742	1.00[CHB][hapmap]
rs11928907	1.00[ASN][1000 genomes]
rs12487438	1.00[CHB][hapmap]
rs13069766	1.00[ASN][1000 genomes]
rs13071132	1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13078237	0.84[AMR][1000 genomes]
rs13084853	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13090504	1.00[ASN][1000 genomes]
rs1498730	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs17313003	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1991440	0.89[EUR][1000 genomes]
rs34006849	1.00[ASN][1000 genomes]
rs34524468	1.00[ASN][1000 genomes]
rs34549392	1.00[ASN][1000 genomes]
rs35098409	1.00[ASN][1000 genomes]
rs35471660	1.00[ASN][1000 genomes]
rs35527623	1.00[ASN][1000 genomes]
rs35558600	1.00[ASN][1000 genomes]
rs35878592	1.00[ASN][1000 genomes]
rs3846052	1.00[ASN][1000 genomes]
rs3913262	1.00[ASN][1000 genomes]
rs4339087	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs5002434	1.00[ASN][1000 genomes]
rs5002435	1.00[ASN][1000 genomes]
rs5002436	1.00[ASN][1000 genomes]
rs5002437	1.00[ASN][1000 genomes]
rs55682444	1.00[ASN][1000 genomes]
rs56019901	1.00[ASN][1000 genomes]
rs59458665	1.00[ASN][1000 genomes]
rs61145443	1.00[ASN][1000 genomes]
rs62271221	1.00[ASN][1000 genomes]
rs6439474	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6439476	1.00[ASN][1000 genomes]
rs6768709	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6772791	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6776727	1.00[ASN][1000 genomes]
rs6784751	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6804439	1.00[ASN][1000 genomes]
rs6809909	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs71331755	1.00[ASN][1000 genomes]
rs72986454	1.00[ASN][1000 genomes]
rs73215399	1.00[ASN][1000 genomes]
rs7609766	1.00[ASN][1000 genomes]
rs7613323	1.00[ASN][1000 genomes]
rs7613440	1.00[ASN][1000 genomes]
rs7613450	1.00[ASN][1000 genomes]
rs7614069	1.00[ASN][1000 genomes]
rs7636249	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7637889	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7638751	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7642519	1.00[ASN][1000 genomes]
rs7647682	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7647778	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7651578	1.00[ASN][1000 genomes]
rs9826364	1.00[CHB][hapmap];1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17312996	COPB2	cis	cerebellum	SCAN
rs17312996	TMEM22	cis	parietal	SCAN
rs17312996	PRR23C	cis	cerebellum	SCAN
rs17312996	CCRL1	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134093600-134095000	Flanking Bivalent TSS/Enh	HepG2	liver
2	chr3:134093600-134095200	Flanking Active TSS	Liver	Liver
3	chr3:134093600-134095600	Enhancers	Small Intestine	intestine
4	chr3:134094000-134095000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:134094000-134095000	Enhancers	Placenta	Placenta
6	chr3:134094000-134096000	Enhancers	Stomach Mucosa	stomach
7	chr3:134094000-134098000	Enhancers	Lung	lung
8	chr3:134094200-134095000	Flanking Active TSS	A549	lung
9	chr3:134094200-134095200	Enhancers	Adipose Nuclei	Adipose
10	chr3:134094200-134095200	Enhancers	Fetal Kidney	kidney
11	chr3:134094200-134096000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:134094200-134096000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:134094200-134098000	Enhancers	Esophagus	oesophagus
14	chr3:134094400-134095000	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr3:134094400-134095200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
16	chr3:134094400-134096000	Enhancers	Pancreas	Pancrea
17	chr3:134094400-134096200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:134094400-134096200	Enhancers	Placenta Amnion	Placenta Amnion
19	chr3:134094400-134096200	Enhancers	HMEC	breast
20	chr3:134094400-134096600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:134094400-134097000	Weak transcription	Brain Anterior Caudate	brain
22	chr3:134094400-134097200	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:134094400-134098000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:134094400-134098200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:134094400-134101400	Weak transcription	Aorta	Aorta
26	chr3:134094600-134095000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr3:134094600-134095000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
28	chr3:134094600-134095000	Enhancers	Fetal Heart	heart
29	chr3:134094600-134095600	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr3:134094600-134095800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:134094600-134096000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:134094600-134096000	Enhancers	Colonic Mucosa	Colon
33	chr3:134094600-134096200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
34	chr3:134094600-134096200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
35	chr3:134094600-134096200	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr3:134094600-134096400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:134094600-134096600	Weak transcription	Right Ventricle	heart
38	chr3:134094600-134096800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:134094600-134096800	Weak transcription	Brain Angular Gyrus	brain
40	chr3:134094600-134096800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr3:134094600-134097000	Weak transcription	Psoas Muscle	Psoas
42	chr3:134094600-134097000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:134094600-134097200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:134094600-134097200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:134094600-134097200	Weak transcription	Right Atrium	heart
46	chr3:134094600-134097400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
47	chr3:134094600-134097400	Enhancers	Fetal Intestine Large	intestine
48	chr3:134094600-134097400	Enhancers	Fetal Intestine Small	intestine
49	chr3:134094600-134098200	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr3:134094600-134098200	Enhancers	NHEK	skin

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