Variant report

Variant	rs1170390
Chromosome Location	chr3:145863779-145863780
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	chr3:145862765..145866552-chr3:145878072..145880810,4	MCF-7	breast:
2	chr3:145863564..145865449-chr3:145867210..145869807,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10935601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10935602	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10935604	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10935606	0.85[ASW][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap]
rs1170389	0.81[CHB][hapmap];0.82[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs1170391	0.81[CHB][hapmap];0.83[JPT][hapmap];0.90[YRI][hapmap]
rs1170393	0.81[CHB][hapmap];0.83[JPT][hapmap];0.90[YRI][hapmap]
rs11717610	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11718741	0.83[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs12485283	0.94[JPT][hapmap]
rs12492656	0.86[EUR][1000 genomes]
rs12498084	0.86[AFR][1000 genomes]
rs13087364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13088180	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1375580	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1375591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1449443	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1449446	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16857897	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs16857919	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1707468	0.86[AFR][1000 genomes]
rs1707469	0.85[ASW][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs17413767	0.86[AFR][1000 genomes]
rs1868541	0.85[ASW][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.90[YRI][hapmap]
rs1982382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2175668	0.84[GIH][hapmap];0.88[JPT][hapmap]
rs3762694	0.84[EUR][1000 genomes]
rs3792340	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3792345	0.81[EUR][1000 genomes]
rs3804663	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs3804667	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4611785	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4681293	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4681297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4681301	0.83[JPT][hapmap]
rs56686359	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57327675	0.86[AFR][1000 genomes]
rs60811409	0.85[AFR][1000 genomes]
rs6771106	0.83[EUR][1000 genomes]
rs6771118	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6775684	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6781300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6783926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6792464	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]
rs6794727	0.84[EUR][1000 genomes]
rs7613150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7628805	0.94[JPT][hapmap];0.83[MEX][hapmap]
rs7642940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9820945	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]
rs9823126	0.83[EUR][1000 genomes]
rs9836725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9869137	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv877613	chr3:145833232-145912055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv1011146	chr3:145859022-145911429	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv1012485	chr3:145861750-145947125	Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv536758	chr3:145861750-145947125	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1170390	PLOD2	cis	parietal	SCAN
rs1170390	HLTF	cis	parietal	SCAN
rs1170390	SLC9A9	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145832000-145870800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:145835800-145874000	Weak transcription	Psoas Muscle	Psoas
3	chr3:145840400-145874000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:145850400-145864400	Weak transcription	HMEC	breast
5	chr3:145851600-145864200	Weak transcription	Right Atrium	heart
6	chr3:145856400-145864200	Weak transcription	Left Ventricle	heart
7	chr3:145856400-145875800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:145858800-145866400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr3:145860400-145875600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:145860600-145868800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:145860800-145864200	Weak transcription	Gastric	stomach
12	chr3:145860800-145866000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:145860800-145866200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:145860800-145870000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:145860800-145873800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:145860800-145874000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:145860800-145874000	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:145861000-145869000	Weak transcription	Fetal Intestine Large	intestine
19	chr3:145861000-145870200	Weak transcription	Brain Anterior Caudate	brain
20	chr3:145861000-145876400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:145861400-145865600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:145861400-145866000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:145861400-145866200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:145861400-145866400	Weak transcription	NHDF-Ad	bronchial
25	chr3:145861400-145870200	Weak transcription	Small Intestine	intestine
26	chr3:145861400-145870600	Weak transcription	NH-A	brain
27	chr3:145861600-145864200	Weak transcription	HepG2	liver
28	chr3:145861600-145869000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:145861600-145870000	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:145861800-145864200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:145861800-145864200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:145861800-145864200	Weak transcription	Ovary	ovary
33	chr3:145861800-145864200	Weak transcription	Right Ventricle	heart
34	chr3:145861800-145864600	Enhancers	Stomach Smooth Muscle	stomach
35	chr3:145861800-145865200	Weak transcription	Fetal Intestine Small	intestine
36	chr3:145861800-145866600	Weak transcription	Aorta	Aorta
37	chr3:145861800-145866800	Weak transcription	Fetal Kidney	kidney
38	chr3:145861800-145867600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:145861800-145870200	Weak transcription	Brain Substantia Nigra	brain
40	chr3:145861800-145870400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:145861800-145870800	Weak transcription	Pancreas	Pancrea
42	chr3:145861800-145872200	Weak transcription	Adipose Nuclei	Adipose
43	chr3:145861800-145873800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:145861800-145873800	Weak transcription	HSMMtube	muscle
45	chr3:145861800-145874000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:145861800-145874000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr3:145862000-145864200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:145862000-145864200	Weak transcription	Liver	Liver
49	chr3:145862000-145866000	Weak transcription	Fetal Lung	lung
50	chr3:145862000-145871600	Strong transcription	HSMM	muscle

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