Variant report

Variant	rs6791142
Chromosome Location	chr3:136377377-136377378
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	chr3:136364480..136366014-chr3:136376930..136379520,2	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	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10513014	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs1070232	0.93[JPT][hapmap]
rs10935185	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
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];0.90[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11715257	0.87[JPT][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];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12163529	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12486911	1.00[YRI][hapmap]
rs12630999	0.93[JPT][hapmap]
rs12635723	0.93[JPT][hapmap]
rs1394092	0.93[JPT][hapmap]
rs1681817	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.90[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]
rs2062322	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]
rs2688600	0.84[AMR][1000 genomes]
rs2688601	0.84[AMR][1000 genomes]
rs34438032	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3856637	0.93[JPT][hapmap]
rs4038578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4038587	0.92[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
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];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
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];0.90[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]
rs4630889	0.87[AMR][1000 genomes]
rs4678433	0.93[JPT][hapmap]
rs4678436	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4678437	0.93[JPT][hapmap]
rs4678438	0.93[JPT][hapmap]
rs55970317	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
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];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
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]
rs6764567	0.81[EUR][1000 genomes]
rs6789329	1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][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];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6808312	0.93[JPT][hapmap];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs699165	0.93[JPT][hapmap]
rs711975	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs73228043	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7427564	0.90[AMR][1000 genomes]
rs7432375	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
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];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7618518	1.00[ASW][hapmap];1.00[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];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
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];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7621025	0.93[JPT][hapmap]
rs7634476	0.89[ASN][1000 genomes]
rs7637129	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
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];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs940174	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];0.92[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
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];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9845762	0.93[JPT][hapmap]
rs9854084	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
rs6791142	PCCB	Cis_1M	lymphoblastoid	RTeQTL
rs6791142	PCCB	cis	multi-tissue	Pritchard
rs6791142	PCCB	cis	lymphoblastoid	seeQTL
rs6791142	MSL2	cis	parietal	SCAN
rs6791142	PCCB	cis	parietal	SCAN
rs6791142	SPSB4	cis	cerebellum	SCAN
rs6791142	PCCB	cis	cerebellum	SCAN
rs6791142	DBR1	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136357800-136387400	Weak transcription	Fetal Thymus	thymus
2	chr3:136364800-136377800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:136365000-136396400	Weak transcription	Gastric	stomach
4	chr3:136365200-136381400	Weak transcription	Pancreas	Pancrea
5	chr3:136368200-136385000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:136369000-136386800	Weak transcription	Lung	lung
7	chr3:136370600-136385400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:136370800-136382800	Weak transcription	Ovary	ovary
9	chr3:136372000-136383200	Weak transcription	Aorta	Aorta
10	chr3:136373800-136377600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:136373800-136382600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:136374200-136377800	Weak transcription	Fetal Kidney	kidney
13	chr3:136374400-136382600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:136374400-136387400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:136374400-136390000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:136374600-136378200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:136374600-136381200	Weak transcription	Fetal Stomach	stomach
18	chr3:136374600-136384200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:136374600-136387400	Weak transcription	Primary T cells from cord blood	blood
20	chr3:136374600-136389400	Weak transcription	Fetal Intestine Small	intestine
21	chr3:136374800-136377800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:136374800-136383400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:136374800-136390000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:136375600-136390400	Weak transcription	Dnd41	blood
25	chr3:136376400-136377600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:136376400-136377800	Enhancers	Brain Hippocampus Middle	brain
27	chr3:136376400-136387400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr3:136376600-136377600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:136376600-136377600	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr3:136376600-136377600	Weak transcription	Adipose Nuclei	Adipose
31	chr3:136376600-136377600	Weak transcription	Brain Anterior Caudate	brain
32	chr3:136376600-136377800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:136376600-136377800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:136376600-136377800	Weak transcription	Psoas Muscle	Psoas
35	chr3:136376600-136392200	Weak transcription	Placenta	Placenta
36	chr3:136376800-136377600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:136376800-136381200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:136376800-136390400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:136377000-136377600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:136377000-136377800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:136377000-136386800	Weak transcription	Left Ventricle	heart
42	chr3:136377000-136387600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:136377000-136389400	Weak transcription	NHEK	skin
44	chr3:136377000-136390400	Weak transcription	Right Ventricle	heart

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