Variant report

Variant	rs8177272
Chromosome Location	chr3:133482870-133482871
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CREB1	chr3:133482430-133483252	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:133470213-133490385	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:133482564-133483225	HepG2	liver:	n/a	n/a
4	HEY1	chr3:133482710-133483065	HepG2	liver:	n/a	n/a
5	MBD4	chr3:133482345-133483652	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:133482335-133484568	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:133482405-133483641	HepG2	liver:	n/a	n/a
8	FOSL2	chr3:133482442-133483395	HepG2	liver:	n/a	n/a
9	NFIC	chr3:133482605-133483155	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:133471516-133487597	HepG2	liver:	n/a	n/a
11	HEY1	chr3:133482177-133483767	HepG2	liver:	n/a	n/a
12	MBD4	chr3:133479369-133483413	HepG2	liver:	n/a	n/a
13	POLR2A	chr3:133480882-133484500	HepG2	liver:	n/a	n/a
14	POLR2A	chr3:133479294-133484913	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:133482481-133484475	HepG2	liver:	n/a	n/a
16	POLR2A	chr3:133470633-133487808	HepG2	liver:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:133482007..133483955-chr3:133484713..133486913,2	MCF-7	breast:
2	chr3:133475218..133478981-chr3:133481312..133484055,3	K562	blood:

No data

Variant related genes	Relation type
TF	TF binding region
ENSG00000091513	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12490148	0.84[CEU][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs12595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12769	0.81[AMR][1000 genomes]
rs1358024	0.90[CHB][hapmap];0.88[CHD][hapmap];0.84[ASN][1000 genomes]
rs1525889	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1830083	0.81[AMR][1000 genomes]
rs1830084	0.81[AMR][1000 genomes]
rs1880669	0.86[CHD][hapmap]
rs2692695	0.87[CHD][hapmap]
rs34252038	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34805309	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3811647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811658	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4854760	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4854761	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4854762	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6439439	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6762719	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6794945	0.88[CEU][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs6797713	0.81[AMR][1000 genomes]
rs7638018	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8177224	0.81[CHD][hapmap];0.91[MEX][hapmap]
rs8177240	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8177245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8177247	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8177248	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8177252	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8177253	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8177256	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8177259	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8177260	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8177261	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8177262	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8177271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8177295	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8177297	0.80[ASN][1000 genomes]
rs9813689	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9843728	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9871148	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9882812	0.81[AMR][1000 genomes];0.81[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	nsv877506	chr3:133423473-133569777	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8177272	ANAPC13	cis	parietal	SCAN
rs8177272	SRPRB	cis	parietal	SCAN
rs8177272	TOPBP1	cis	parietal	SCAN
rs8177272	SRPRB	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133465600-133483000	Weak transcription	Brain Germinal Matrix	brain
2	chr3:133475000-133487000	Weak transcription	Fetal Brain Male	brain
3	chr3:133477000-133490400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:133480000-133483800	Weak transcription	Adipose Nuclei	Adipose
5	chr3:133480400-133486000	Genic enhancers	Brain Substantia Nigra	brain
6	chr3:133480800-133485200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:133480800-133490000	Genic enhancers	HepG2	liver
8	chr3:133482400-133483600	Genic enhancers	Brain Anterior Caudate	brain
9	chr3:133482400-133485200	Genic enhancers	Brain Hippocampus Middle	brain
10	chr3:133482400-133485600	Genic enhancers	Brain Cingulate Gyrus	brain
11	chr3:133482600-133483000	Enhancers	Esophagus	oesophagus
12	chr3:133482600-133483000	Enhancers	Left Ventricle	heart
13	chr3:133482600-133483000	Enhancers	Right Ventricle	heart
14	chr3:133482600-133483200	Enhancers	Fetal Muscle Trunk	muscle
15	chr3:133482600-133483600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:133482600-133483600	Enhancers	Right Atrium	heart
17	chr3:133482600-133484000	Enhancers	HSMMtube	muscle
18	chr3:133482600-133484200	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr3:133482600-133484400	Genic enhancers	Liver	Liver
20	chr3:133482600-133484400	Enhancers	Fetal Lung	lung
21	chr3:133482600-133484600	Enhancers	Fetal Muscle Leg	muscle
22	chr3:133482600-133485400	Genic enhancers	Brain Inferior Temporal Lobe	brain
23	chr3:133482800-133483200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr3:133482800-133483800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:133482800-133484000	Enhancers	Fetal Stomach	stomach
26	chr3:133482800-133484200	Genic enhancers	Brain Angular Gyrus	brain

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