Variant report

Variant	rs6792464
Chromosome Location	chr3:145784631-145784632
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:145782122..145785411-chr3:145878106..145882365,5	MCF-7	breast:
2	chr3:145783644..145786560-chr3:145833867..145835451,2	MCF-7	breast:
3	chr3:145783528..145785150-chr3:145794804..145797191,2	MCF-7	breast:
4	chr3:145779679..145784840-chr3:145877412..145880527,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10935601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10935602	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10935604	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs10935606	0.82[JPT][hapmap]
rs1170389	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1170390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1170391	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs1170393	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs11717610	0.84[EUR][1000 genomes]
rs11718741	0.83[JPT][hapmap]
rs12485283	0.94[JPT][hapmap]
rs13087364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13088180	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375580	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1375591	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1449443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1449446	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16857897	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16857919	0.83[EUR][1000 genomes]
rs1707469	0.81[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap]
rs1868541	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs1982382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2175668	0.88[JPT][hapmap]
rs3762694	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3792340	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792345	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3804663	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3804667	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4611785	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681293	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681297	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4681301	0.83[JPT][hapmap]
rs56686359	0.84[EUR][1000 genomes]
rs6440420	0.92[YRI][hapmap]
rs6771106	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6771118	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6783926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6794727	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7613150	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs7628805	0.94[JPT][hapmap]
rs7642940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9820945	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9836725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869137	1.00[CHB][hapmap];1.00[JPT][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]
rs9881772	0.84[YRI][hapmap]

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	nsv877584	chr3:144903957-145833232	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv525829	chr3:145614317-145863779	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv4046	chr3:145693249-145880189	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6792464	PLOD2	cis	parietal	SCAN
rs6792464	SLC9A9	cis	parietal	SCAN
rs6792464	HLTF	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145762800-145785000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:145768800-145788400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:145774600-145787200	Weak transcription	Esophagus	oesophagus
4	chr3:145774600-145795400	Weak transcription	Aorta	Aorta
5	chr3:145775400-145786600	Weak transcription	HepG2	liver
6	chr3:145776200-145786000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:145776200-145786400	Weak transcription	Adipose Nuclei	Adipose
8	chr3:145776600-145787200	Weak transcription	HMEC	breast
9	chr3:145777000-145819400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:145778200-145817200	Weak transcription	Fetal Stomach	stomach
11	chr3:145778600-145789000	Weak transcription	Left Ventricle	heart
12	chr3:145778800-145788400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:145779000-145789600	Weak transcription	Fetal Heart	heart
14	chr3:145779400-145788800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:145779600-145820600	Weak transcription	Fetal Kidney	kidney
16	chr3:145780000-145815600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:145780600-145820400	Weak transcription	Placenta	Placenta
18	chr3:145780800-145786600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:145780800-145793800	Weak transcription	Ovary	ovary
20	chr3:145780800-145793800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:145780800-145819800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:145781000-145788400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:145781000-145788800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:145781800-145785000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:145781800-145831800	Weak transcription	Psoas Muscle	Psoas
26	chr3:145782000-145785400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:145782600-145786200	Weak transcription	Liver	Liver
28	chr3:145782600-145786400	Weak transcription	Fetal Intestine Large	intestine
29	chr3:145782800-145843200	Weak transcription	Pancreas	Pancrea
30	chr3:145783000-145785000	Weak transcription	HUVEC	blood vessel
31	chr3:145783200-145785600	Genic enhancers	Muscle Satellite Cultured Cells	--
32	chr3:145783600-145785400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:145783600-145785600	Enhancers	NHDF-Ad	bronchial
34	chr3:145783600-145785800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:145783600-145785800	Genic enhancers	Osteobl	bone
36	chr3:145783800-145786400	Weak transcription	Fetal Lung	lung
37	chr3:145784000-145785400	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr3:145784000-145789400	Weak transcription	Colon Smooth Muscle	Colon
39	chr3:145784000-145811800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:145784200-145785200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:145784200-145785400	Flanking Active TSS	A549	lung
42	chr3:145784200-145785400	Genic enhancers	HSMM	muscle
43	chr3:145784400-145785400	Enhancers	HSMMtube	muscle
44	chr3:145784400-145788400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:145784600-145785200	Enhancers	NH-A	brain
46	chr3:145784600-145790400	Weak transcription	NHLF	lung
47	chr3:145784600-145848800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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