Variant report

Variant	rs361253
Chromosome Location	chr3:136704568-136704569
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	chr3:136697313..136700260-chr3:136703197..136704911,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174564	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs108858	0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs10935213	0.84[LWK][hapmap]
rs11711599	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054220	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12629000	1.00[CHB][hapmap]
rs13095028	0.90[CHD][hapmap];0.85[JPT][hapmap]
rs13095034	0.87[ASN][1000 genomes]
rs1385306	0.82[ASN][1000 genomes]
rs1406539	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1620455	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1654900	0.82[ASN][1000 genomes]
rs1654901	0.82[ASN][1000 genomes]
rs1654924	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1654925	0.84[LWK][hapmap]
rs1682339	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1682361	0.82[ASN][1000 genomes]
rs1682362	0.82[ASN][1000 genomes]
rs1682363	0.82[ASN][1000 genomes]
rs1682364	0.82[ASN][1000 genomes]
rs1682365	0.82[ASN][1000 genomes]
rs1682366	0.82[ASN][1000 genomes]
rs16844241	1.00[CHB][hapmap]
rs168635	0.80[LWK][hapmap]
rs171519	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs181732	0.82[ASN][1000 genomes]
rs183120	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183121	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2117008	0.83[ASN][1000 genomes]
rs2344092	0.84[ASN][1000 genomes]
rs361227	0.82[ASN][1000 genomes]
rs361228	0.82[ASN][1000 genomes]
rs361229	0.82[ASN][1000 genomes]
rs361232	0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs361233	0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs361234	0.85[ASN][1000 genomes]
rs361235	0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs361237	0.81[LWK][hapmap];0.81[MKK][hapmap]
rs361238	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361239	0.87[LWK][hapmap]
rs361240	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361243	0.87[LWK][hapmap]
rs361245	0.84[LWK][hapmap]
rs361249	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4678275	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4678447	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs55781515	0.82[ASN][1000 genomes]
rs71620537	0.87[ASN][1000 genomes]
rs75977	0.87[LWK][hapmap]
rs7610507	1.00[CHB][hapmap]
rs7631541	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7648198	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap]
rs835627	0.82[ASN][1000 genomes]
rs835629	0.82[ASN][1000 genomes]
rs835630	0.82[ASN][1000 genomes]
rs835631	0.82[ASN][1000 genomes]
rs835636	1.00[CHD][hapmap]
rs835637	1.00[CHD][hapmap]
rs835638	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs835652	0.86[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs9681468	0.81[ASN][1000 genomes]
rs9682783	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9845076	0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs9845460	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9850024	0.82[ASN][1000 genomes]
rs9854795	0.82[ASN][1000 genomes]
rs9874615	0.82[ASN][1000 genomes]
rs9875855	0.87[ASN][1000 genomes]
rs999038	0.82[ASN][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	nsv877534	chr3:136676303-136765859	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv524856	chr3:136693459-137190765	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1012111	chr3:136695367-137343430	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs361253	PCCB	cis	cerebellum	SCAN
rs361253	PPP2R3A	cis	parietal	SCAN
rs361253	PCCB	cis	parietal	SCAN
rs361253	IL20RB	cis	Skin Sun Exposed Lower leg	GTEx
rs361253	SPSB4	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136695400-136706200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:136699800-136705400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:136701000-136704800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:136701600-136705200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:136702000-136705600	Enhancers	Fetal Thymus	thymus
6	chr3:136702200-136705600	Enhancers	Thymus	Thymus
7	chr3:136703000-136704600	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr3:136703000-136704600	Enhancers	HSMM	muscle
9	chr3:136703000-136704800	Enhancers	HMEC	breast
10	chr3:136703200-136704800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr3:136703400-136704800	Enhancers	Fetal Intestine Large	intestine
12	chr3:136703600-136704600	Enhancers	Fetal Intestine Small	intestine
13	chr3:136703600-136704600	Transcr. at gene 5' and 3'	NHEK	skin
14	chr3:136703600-136705000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:136703800-136706400	Weak transcription	Esophagus	oesophagus
16	chr3:136703800-136706600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:136703800-136706600	Weak transcription	Lung	lung
18	chr3:136703800-136708400	Weak transcription	Colonic Mucosa	Colon
19	chr3:136703800-136708400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:136703800-136713600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:136703800-136732400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:136704000-136706400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:136704000-136708800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:136704000-136713200	Weak transcription	Right Atrium	heart
25	chr3:136704000-136713400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:136704000-136713400	Weak transcription	Pancreas	Pancrea
27	chr3:136704000-136714600	Weak transcription	Right Ventricle	heart
28	chr3:136704000-136730600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:136704200-136704600	Enhancers	Hela-S3	cervix
30	chr3:136704200-136704800	Enhancers	HSMMtube	muscle
31	chr3:136704200-136708400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:136704200-136713200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:136704200-136713200	Weak transcription	Small Intestine	intestine
34	chr3:136704400-136707400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:136704400-136713400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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