Variant report

Variant	rs4521165
Chromosome Location	chr3:136369710-136369711
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	chr3:136365030..136366947-chr3:136367021..136371094,3	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1017882	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10513014	0.92[CHB][hapmap]
rs1070228	0.82[EUR][1000 genomes]
rs1070232	1.00[JPT][hapmap]
rs10935185	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10935186	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11715257	0.93[JPT][hapmap]
rs11919030	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12163529	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12486911	1.00[YRI][hapmap]
rs12630999	1.00[JPT][hapmap]
rs12635723	1.00[JPT][hapmap]
rs1394092	1.00[JPT][hapmap]
rs1681817	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1729951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs2062322	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2688600	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2688601	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34438032	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856637	1.00[JPT][hapmap]
rs4038578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs4038587	0.92[CEU][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4408829	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4630889	0.88[AMR][1000 genomes]
rs4678433	1.00[JPT][hapmap]
rs4678436	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4678437	1.00[JPT][hapmap]
rs4678438	1.00[JPT][hapmap]
rs55970317	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6439649	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439655	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs6789329	1.00[CHB][hapmap];0.93[CHD][hapmap]
rs6791142	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6794351	1.00[JPT][hapmap]
rs6802702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6808312	1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs699165	1.00[JPT][hapmap]
rs711975	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs73228043	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7427564	0.91[AMR][1000 genomes]
rs7432375	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7616204	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7618518	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618871	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7621025	1.00[JPT][hapmap]
rs7634476	0.89[ASN][1000 genomes]
rs7637129	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs833752	1.00[JPT][hapmap]
rs900048	0.93[JPT][hapmap]
rs900818	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs940174	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9836231	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9845762	1.00[JPT][hapmap]
rs9854084	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1008866	chr3:136364511-136427790	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv877529	chr3:136364511-136487559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4521165	PCCB	cis	multi-tissue	Pritchard
rs4521165	PCCB	cis	cerebellum	SCAN
rs4521165	DBR1	cis	cerebellum	SCAN
rs4521165	PCCB	cis	lymphoblastoid	seeQTL
rs4521165	PCCB	Cis_1M	lymphoblastoid	RTeQTL
rs4521165	SPSB4	cis	cerebellum	SCAN
rs4521165	PCCB	cis	parietal	SCAN
rs4521165	MSL2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136348800-136373600	Weak transcription	Thymus	Thymus
2	chr3:136349800-136372400	Weak transcription	Dnd41	blood
3	chr3:136350600-136372200	Weak transcription	Primary T cells from cord blood	blood
4	chr3:136351600-136376200	Weak transcription	Esophagus	oesophagus
5	chr3:136352400-136371600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:136352400-136371600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:136352400-136371800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:136357800-136387400	Weak transcription	Fetal Thymus	thymus
9	chr3:136364600-136371800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:136364800-136372200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:136364800-136377800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:136365000-136370000	Weak transcription	Ovary	ovary
13	chr3:136365000-136396400	Weak transcription	Gastric	stomach
14	chr3:136365200-136369800	Weak transcription	K562	blood
15	chr3:136365200-136370000	Weak transcription	Psoas Muscle	Psoas
16	chr3:136365200-136370600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr3:136365200-136381400	Weak transcription	Pancreas	Pancrea
18	chr3:136367200-136369800	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:136367400-136371000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:136368000-136370600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr3:136368200-136371400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:136368200-136385000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:136369000-136371800	Weak transcription	Fetal Intestine Small	intestine
24	chr3:136369000-136386800	Weak transcription	Lung	lung
25	chr3:136369600-136369800	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr3:136369600-136370400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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