Variant report

Variant	rs2062322
Chromosome Location	chr3:136408886-136408887
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	chr3:136389835..136392302-chr3:136408179..136409824,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10513014	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs1070232	0.93[JPT][hapmap]
rs10935186	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap]
rs11919030	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[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]
rs12486911	1.00[YRI][hapmap]
rs12630999	0.93[JPT][hapmap]
rs12635723	0.93[JPT][hapmap]
rs1681817	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1729951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs3856637	0.93[JPT][hapmap]
rs4038578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4038587	0.92[CEU][hapmap]
rs4408829	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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]
rs4521165	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]
rs4678433	0.93[JPT][hapmap]
rs4678437	0.93[JPT][hapmap]
rs4678438	0.93[JPT][hapmap]
rs6439649	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[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6439655	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs6789329	1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap]
rs6791142	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6794351	0.93[JPT][hapmap]
rs6802702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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]
rs6808312	0.93[JPT][hapmap]
rs699165	0.93[JPT][hapmap]
rs711975	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs7432375	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap]
rs7616204	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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]
rs7618518	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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]
rs7618871	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7621025	0.93[JPT][hapmap]
rs833752	0.93[JPT][hapmap]
rs900048	0.87[JPT][hapmap]
rs900818	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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]
rs940174	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9836231	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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]
rs9845762	0.93[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
rs2062322	PCCB	cis	cerebellum	SCAN
rs2062322	PCCB	Cis_1M	lymphoblastoid	RTeQTL
rs2062322	MSL2	cis	parietal	SCAN
rs2062322	PCCB	cis	parietal	SCAN
rs2062322	PCCB	cis	multi-tissue	Pritchard
rs2062322	PCCB	cis	lymphoblastoid	seeQTL
rs2062322	SPSB4	cis	cerebellum	SCAN
rs2062322	DBR1	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136381800-136410800	Weak transcription	Psoas Muscle	Psoas
2	chr3:136386400-136412800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:136387200-136412400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:136390200-136413000	Weak transcription	Pancreas	Pancrea
5	chr3:136390600-136412000	Weak transcription	Thymus	Thymus
6	chr3:136390800-136447800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:136394200-136409800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:136395000-136410200	Weak transcription	Small Intestine	intestine
9	chr3:136395000-136418200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:136396600-136411800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr3:136398600-136410200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:136400600-136412000	Weak transcription	Primary B cells from cord blood	blood
13	chr3:136402400-136409000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr3:136403600-136410800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:136404800-136410600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:136405000-136412400	Weak transcription	Fetal Intestine Small	intestine
17	chr3:136405400-136409200	Weak transcription	K562	blood
18	chr3:136405400-136410200	Weak transcription	Left Ventricle	heart
19	chr3:136405400-136413000	Weak transcription	Fetal Heart	heart
20	chr3:136405600-136410200	Weak transcription	GM12878-XiMat	blood
21	chr3:136406200-136409800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:136407400-136409600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:136407600-136409000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr3:136407600-136409800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:136407600-136410600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr3:136407600-136411800	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr3:136407800-136412400	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:136408000-136409200	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr3:136408000-136409800	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr3:136408200-136411600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:136408400-136409000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr3:136408400-136409600	Enhancers	HepG2	liver
33	chr3:136408400-136411600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:136408600-136409400	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr3:136408600-136409400	Enhancers	Adipose Nuclei	Adipose
36	chr3:136408600-136409400	Enhancers	Lung	lung
37	chr3:136408600-136410600	Enhancers	Primary T cells fromperipheralblood	blood
38	chr3:136408800-136410200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:136408800-136410600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:136408800-136412200	Weak transcription	Fetal Muscle Leg	muscle
41	chr3:136408800-136412400	Weak transcription	Right Atrium	heart
42	chr3:136408800-136414600	Weak transcription	Gastric	stomach

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