Variant report

Variant	rs1560415
Chromosome Location	chr3:156537358-156537359
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr3:156536076-156537391	Hela-S3	cervix:	n/a	chr3:156536612-156536621 chr3:156536139-156536150

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:156500704..156502308-chr3:156536284..156537866,2	MCF-7	breast:
2	chr3:156536226..156539045-chr3:156559314..156561294,2	MCF-7	breast:
3	chr3:156388866..156397270-chr3:156524172..156537549,71	MCF-7	breast:
4	chr3:156509352..156512043-chr3:156536424..156537930,2	K562	blood:
5	chr3:156530292..156533416-chr3:156536221..156538650,3	MCF-7	breast:
6	chr14:55513055..55515662-chr3:156536623..156538871,2	MCF-7	breast:
7	chr3:156537180..156540050-chr3:156547950..156549740,2	K562	blood:
8	chr3:156533566..156537799-chr3:156875553..156879495,5	MCF-7	breast:

No data

Variant related genes	Relation type
LINC00886	TF binding region
ENSG00000163660	Chromatin interaction
ENSG00000243926	Chromatin interaction
ENSG00000163659	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10936037	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10936038	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11707914	0.88[EUR][1000 genomes]
rs11711674	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11717133	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492804	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12492968	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12497539	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13072896	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13086516	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13097325	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1430410	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1430411	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1560416	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1835372	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2060015	0.81[EUR][1000 genomes]
rs3910072	0.81[EUR][1000 genomes]
rs4680305	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59717073	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776157	0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7638625	0.82[EUR][1000 genomes]
rs7641929	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9812169	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9818684	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9820830	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9837271	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842198	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9847187	0.81[EUR][1000 genomes]
rs9858861	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9876010	0.81[EUR][1000 genomes]

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	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1560415	LINC00886	cis	Nerve Tibial	GTEx
rs1560415	LINC00886	cis	Adipose Subcutaneous	GTEx
rs1560415	LINC00886	cis	Muscle Skeletal	GTEx
rs1560415	LINC00886	cis	Artery Tibial	GTEx
rs1560415	LINC00886	cis	Esophagus Muscularis	GTEx
rs1560415	LINC00886	cis	Esophagus Mucosa	GTEx
rs1560415	LINC00886	cis	Artery Aorta	GTEx
rs1560415	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs1560415	LINC00886	cis	lung	GTEx
rs1560415	LINC00886	cis	Thyroid	GTEx
rs1560415	LINC00886	cis	Stomach	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156535400-156538800	Weak transcription	Lung	lung
2	chr3:156535400-156539000	Enhancers	HSMM	muscle
3	chr3:156535400-156539200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:156535400-156543400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:156535600-156538000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:156535600-156538600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr3:156535600-156538600	Enhancers	NHLF	lung
8	chr3:156535600-156538800	Enhancers	HSMMtube	muscle
9	chr3:156535600-156538800	Enhancers	NHDF-Ad	bronchial
10	chr3:156535600-156539000	Enhancers	HMEC	breast
11	chr3:156535600-156539000	Enhancers	HUVEC	blood vessel
12	chr3:156535800-156537600	Enhancers	K562	blood
13	chr3:156535800-156537800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:156536200-156538000	Weak transcription	Stomach Mucosa	stomach
15	chr3:156536200-156538800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:156536200-156539000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr3:156536200-156543200	Weak transcription	Fetal Kidney	kidney
18	chr3:156536400-156538800	Enhancers	NHEK	skin
19	chr3:156536400-156539000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:156536400-156539000	Enhancers	Hela-S3	cervix
21	chr3:156536400-156539000	Enhancers	Osteobl	bone
22	chr3:156536400-156542400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:156536400-156542400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:156536400-156543000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:156536400-156543200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:156536400-156543200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr3:156536400-156543200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr3:156536400-156543200	Weak transcription	Thymus	Thymus
29	chr3:156536600-156537600	Flanking Active TSS	A549	lung
30	chr3:156536600-156541600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr3:156536800-156541800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:156537000-156537400	Enhancers	GM12878-XiMat	blood
33	chr3:156537000-156537400	Enhancers	HepG2	liver
34	chr3:156537000-156539000	Enhancers	NH-A	brain
35	chr3:156537000-156540400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:156537000-156540400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:156537000-156541800	Weak transcription	Fetal Intestine Small	intestine
38	chr3:156537000-156543200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:156537000-156543400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:156537000-156543400	Weak transcription	Liver	Liver
41	chr3:156537000-156543600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:156537000-156543600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:156537200-156537600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:156537200-156538800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:156537200-156541000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:156537200-156542600	Weak transcription	Duodenum Mucosa	Duodenum

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