Variant report

Variant	rs1707469
Chromosome Location	chr3:145861305-145861306
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:145860639..145862586-chr3:145877075..145878969,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10935601	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs10935605	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10935606	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10935608	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1170389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1170390	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]
rs1170391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1170392	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1170393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718741	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11927021	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12498084	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13087364	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs13088646	0.89[JPT][hapmap]
rs1375588	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1375591	0.81[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap]
rs1707468	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17413767	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1868541	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1913186	0.86[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap]
rs1982382	0.81[JPT][hapmap]
rs4342076	0.82[GIH][hapmap]
rs4681297	0.81[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap]
rs4681301	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56842856	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57327675	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57945878	0.80[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60267871	0.80[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60811409	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61050446	0.80[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61154334	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6771118	0.81[CHB][hapmap]
rs6781300	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6792464	0.81[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap]
rs71304237	0.92[EUR][1000 genomes]
rs73148985	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73148986	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73148991	0.80[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7613150	0.81[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap]
rs7623263	0.80[GIH][hapmap];0.89[JPT][hapmap]
rs7642940	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs965032	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9820945	0.81[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap]
rs9836725	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs9869137	0.81[CHB][hapmap];0.85[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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1707469	HLTF	cis	parietal	SCAN
rs1707469	PLOD2	cis	parietal	SCAN
rs1707469	PLOD2	Cis_1M	lymphoblastoid	RTeQTL
rs1707469	PLOD2	cis	Muscle Skeletal	GTEx
rs1707469	PLOD2	cis	lymphoblastoid	seeQTL

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	chr3:145853200-145861600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:145855800-145862000	Enhancers	Fetal Stomach	stomach
8	chr3:145856000-145861400	Enhancers	Rectal Smooth Muscle	rectum
9	chr3:145856200-145862200	Enhancers	Fetal Heart	heart
10	chr3:145856400-145864200	Weak transcription	Left Ventricle	heart
11	chr3:145856400-145875800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:145858000-145861800	Enhancers	A549	lung
13	chr3:145858800-145866400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr3:145859200-145862000	Enhancers	NHLF	lung
15	chr3:145860000-145863000	Genic enhancers	Osteobl	bone
16	chr3:145860200-145861400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:145860200-145861400	Enhancers	NHDF-Ad	bronchial
18	chr3:145860200-145861600	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr3:145860200-145861800	Enhancers	Fetal Intestine Small	intestine
20	chr3:145860200-145861800	Enhancers	HSMM	muscle
21	chr3:145860200-145861800	Enhancers	HSMMtube	muscle
22	chr3:145860200-145862000	Enhancers	Muscle Satellite Cultured Cells	--
23	chr3:145860200-145862000	Enhancers	Fetal Lung	lung
24	chr3:145860200-145862000	Enhancers	HUVEC	blood vessel
25	chr3:145860400-145861400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:145860400-145861400	Enhancers	NH-A	brain
27	chr3:145860400-145861600	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr3:145860400-145861800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:145860400-145861800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:145860400-145861800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:145860400-145861800	Enhancers	Adipose Nuclei	Adipose
32	chr3:145860400-145861800	Enhancers	Brain Substantia Nigra	brain
33	chr3:145860400-145861800	Enhancers	Fetal Kidney	kidney
34	chr3:145860400-145862200	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr3:145860400-145875600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:145860600-145861400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr3:145860600-145861400	Enhancers	Small Intestine	intestine
38	chr3:145860600-145861800	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr3:145860600-145862000	Enhancers	Liver	Liver
40	chr3:145860600-145868800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:145860800-145861400	Active TSS	Aorta	Aorta
42	chr3:145860800-145861600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:145860800-145861600	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr3:145860800-145861800	Active TSS	Stomach Smooth Muscle	stomach
45	chr3:145860800-145864200	Weak transcription	Gastric	stomach
46	chr3:145860800-145866000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:145860800-145866200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:145860800-145870000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:145860800-145873800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr3:145860800-145874000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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