Variant report

Variant	rs10935606
Chromosome Location	chr3:145868148-145868149
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	chr3:145863564..145865449-chr3:145867210..145869807,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10935601	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs10935605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935608	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1170389	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1170390	0.85[ASW][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap]
rs1170391	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1170392	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1170393	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11718741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11927021	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12498084	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13087364	0.82[JPT][hapmap]
rs13088646	0.88[JPT][hapmap]
rs1375588	0.87[EUR][1000 genomes]
rs1375591	0.82[JPT][hapmap]
rs1707468	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1707469	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]
rs17413767	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1868541	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[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];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1913186	0.84[GIH][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs2137485	0.87[ASN][1000 genomes]
rs34800183	0.85[ASN][1000 genomes]
rs4342076	0.84[GIH][hapmap]
rs4681297	0.82[JPT][hapmap]
rs4681301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56842856	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57327675	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57945878	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60267871	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60811409	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61050446	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61154334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781300	0.81[JPT][hapmap]
rs6792464	0.82[JPT][hapmap]
rs71304237	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73148985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73148986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73148991	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7613150	0.82[JPT][hapmap]
rs7623263	0.88[JPT][hapmap]
rs7642940	0.82[JPT][hapmap]
rs965032	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9820945	0.82[JPT][hapmap]
rs9836725	0.82[JPT][hapmap]
rs9869137	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10935606	HLTF	cis	parietal	SCAN
rs10935606	NM_018629	cis	multi-tissue	Pritchard
rs10935606	PLOD2	cis	parietal	SCAN
rs10935606	PLOD2	cis	Muscle Skeletal	GTEx
rs10935606	PLOD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:68 , 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	chr3:145856400-145875800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:145860400-145875600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:145860600-145868800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:145860800-145870000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:145860800-145873800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:145860800-145874000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:145860800-145874000	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:145861000-145869000	Weak transcription	Fetal Intestine Large	intestine
12	chr3:145861000-145870200	Weak transcription	Brain Anterior Caudate	brain
13	chr3:145861000-145876400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:145861400-145870200	Weak transcription	Small Intestine	intestine
15	chr3:145861400-145870600	Weak transcription	NH-A	brain
16	chr3:145861600-145869000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:145861600-145870000	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:145861800-145870200	Weak transcription	Brain Substantia Nigra	brain
19	chr3:145861800-145870400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:145861800-145870800	Weak transcription	Pancreas	Pancrea
21	chr3:145861800-145872200	Weak transcription	Adipose Nuclei	Adipose
22	chr3:145861800-145873800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:145861800-145873800	Weak transcription	HSMMtube	muscle
24	chr3:145861800-145874000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:145861800-145874000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:145862000-145871600	Strong transcription	HSMM	muscle
27	chr3:145862000-145873800	Weak transcription	NHLF	lung
28	chr3:145862400-145874000	Weak transcription	Lung	lung
29	chr3:145862600-145870800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr3:145863600-145869000	Weak transcription	Fetal Stomach	stomach
31	chr3:145864400-145869000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:145864400-145870800	Weak transcription	Esophagus	oesophagus
33	chr3:145864400-145870800	Weak transcription	Gastric	stomach
34	chr3:145864400-145872200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr3:145864400-145873000	Genic enhancers	Osteobl	bone
36	chr3:145864600-145870000	Weak transcription	Right Ventricle	heart
37	chr3:145864600-145870800	Weak transcription	Right Atrium	heart
38	chr3:145864800-145870400	Weak transcription	HMEC	breast
39	chr3:145865200-145869000	Enhancers	Rectal Smooth Muscle	rectum
40	chr3:145865600-145869000	Enhancers	Fetal Heart	heart
41	chr3:145865800-145869000	Weak transcription	Left Ventricle	heart
42	chr3:145865800-145870400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:145865800-145870800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:145866200-145868200	Enhancers	Pancreatic Islets	Pancreatic Islet
45	chr3:145866800-145868400	Weak transcription	Ovary	ovary
46	chr3:145866800-145868600	Enhancers	Stomach Smooth Muscle	stomach
47	chr3:145866800-145868800	Enhancers	Fetal Kidney	kidney
48	chr3:145866800-145869000	Enhancers	A549	lung
49	chr3:145866800-145870000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr3:145866800-145870200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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