Variant report

Variant	rs9820945
Chromosome Location	chr3:145818406-145818407
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	chr3:145808540..145810799-chr3:145816596..145819414,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10935601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935602	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10935604	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][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];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1170391	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs1170393	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs11717610	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11718741	0.83[JPT][hapmap]
rs12171307	0.85[AFR][1000 genomes]
rs12485283	0.94[JPT][hapmap]
rs12492656	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13087364	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]
rs13088180	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1375580	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1375591	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1449443	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1449446	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16857897	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16857919	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][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];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2175668	0.82[GIH][hapmap];0.88[JPT][hapmap]
rs3762694	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3792340	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3792345	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3804663	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3804667	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4611785	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4681293	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4681297	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4681301	0.83[JPT][hapmap]
rs56686359	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6440420	0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs6771106	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6771118	0.90[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6775684	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6781300	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]
rs6783926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792464	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]
rs6794727	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7613150	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7628805	0.94[JPT][hapmap]
rs7639115	0.85[AFR][1000 genomes]
rs7642940	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823126	0.84[EUR][1000 genomes]
rs9836725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9869137	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9881772	0.87[LWK][hapmap];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
rs9820945	PLOD2	cis	parietal	SCAN
rs9820945	HLTF	cis	parietal	SCAN
rs9820945	SLC9A9	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145777000-145819400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:145779600-145820600	Weak transcription	Fetal Kidney	kidney
3	chr3:145780600-145820400	Weak transcription	Placenta	Placenta
4	chr3:145780800-145819800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:145781800-145831800	Weak transcription	Psoas Muscle	Psoas
6	chr3:145782800-145843200	Weak transcription	Pancreas	Pancrea
7	chr3:145784600-145848800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:145785200-145819400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr3:145789200-145830800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:145790000-145819800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:145790200-145818600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:145790200-145819400	Weak transcription	Left Ventricle	heart
13	chr3:145790400-145843200	Weak transcription	Right Ventricle	heart
14	chr3:145791600-145833800	Weak transcription	NHDF-Ad	bronchial
15	chr3:145794400-145818800	Weak transcription	Ovary	ovary
16	chr3:145794400-145827000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:145794400-145828000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:145794600-145819200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:145796200-145821400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:145798800-145839200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:145804000-145819200	Weak transcription	NH-A	brain
22	chr3:145808600-145833000	Weak transcription	Fetal Lung	lung
23	chr3:145809200-145821600	Weak transcription	HMEC	breast
24	chr3:145810200-145823400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:145810400-145829000	Weak transcription	NHLF	lung
26	chr3:145810400-145830800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:145810400-145849800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:145810600-145827200	Weak transcription	Small Intestine	intestine
29	chr3:145810800-145851200	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:145812000-145818600	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:145812000-145818800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:145812000-145826000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:145812000-145826800	Weak transcription	Aorta	Aorta
34	chr3:145812200-145818800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:145812200-145818800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:145812200-145819400	Weak transcription	Fetal Heart	heart
37	chr3:145812200-145839200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:145812400-145819400	Weak transcription	Colon Smooth Muscle	Colon
39	chr3:145813400-145819800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr3:145814200-145841000	Weak transcription	Lung	lung
41	chr3:145814600-145828200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:145815600-145824000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:145815600-145824400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:145815600-145825200	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr3:145815600-145825400	Strong transcription	HSMM	muscle
46	chr3:145815800-145830000	Strong transcription	Osteobl	bone
47	chr3:145816000-145818600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:145816000-145820000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:145816000-145836800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:145816400-145842000	Weak transcription	Colonic Mucosa	Colon

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