Variant report

Variant	rs919520
Chromosome Location	chr3:156537119-156537120
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr3:156536655-156537304	SK-N-SH	brain:	n/a	chr3:156536736-156536745
2	GATA3	chr3:156536457-156537261	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:156536718-156537119	SK-N-SH	brain:	n/a	n/a
4	CEBPB	chr3:156536077-156537119	Hela-S3	cervix:	n/a	chr3:156536151-156536159
5	TCF7L2	chr3:156536766-156537167	Hela-S3	cervix:	n/a	n/a
6	CBX3	chr3:156536634-156537235	HCT-116	colon:	n/a	n/a
7	EP300	chr3:156536631-156537300	Hela-S3	cervix:	n/a	chr3:156536736-156536745
8	NR3C1	chr3:156536755-156537134	A549	lung:	n/a	n/a
9	JUND	chr3:156536076-156537391	Hela-S3	cervix:	n/a	chr3:156536612-156536621 chr3:156536139-156536150
10	FOS	chr3:156536705-156537159	HUVEC	blood vessel:	n/a	chr3:156536937-156536948
11	TBP	chr3:156534669-156537155	Hela-S3	cervix:	n/a	n/a
12	STAT3	chr3:156536028-156537175	MCF10A-Er-Src	breast:	n/a	n/a
13	JUND	chr3:156536707-156537280	SK-N-SH	brain:	n/a	n/a
14	SIN3AK20	chr3:156536591-156537237	HCT-116	colon:	n/a	n/a
15	FOSL2	chr3:156536808-156537134	SK-N-SH	brain:	n/a	n/a
16	SP1	chr3:156536545-156537307	HCT-116	colon:	n/a	n/a
17	MAX	chr3:156536691-156537128	Hela-S3	cervix:	n/a	n/a
18	GATA3	chr3:156536529-156537294	A549	lung:	n/a	n/a
19	GATA3	chr3:156536419-156537312	SK-N-SH	brain:	n/a	n/a
20	TCF12	chr3:156536604-156537294	SK-N-SH	brain:	n/a	n/a
21	FOSL2	chr3:156536621-156537208	A549	lung:	n/a	n/a
22	POLR2A	chr3:156536582-156537236	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr3:156533252-156537169	IMR90	lung:	n/a	n/a
24	USF2	chr3:156536789-156537198	Hela-S3	cervix:	n/a	n/a
25	JUND	chr3:156536582-156537236	HCT-116	colon:	n/a	chr3:156536612-156536621
26	GATA2	chr3:156536622-156537194	HUVEC	blood vessel:	n/a	n/a
27	FOS	chr3:156536616-156537134	MCF10A-Er-Src	breast:	n/a	chr3:156536937-156536948
28	TCF12	chr3:156536578-156537319	SK-N-SH	brain:	n/a	n/a
29	MAZ	chr3:156536719-156537122	Hela-S3	cervix:	n/a	n/a
30	MXI1	chr3:156537003-156537140	K562	blood:	n/a	n/a
31	FOSL1	chr3:156536602-156537288	HCT-116	colon:	n/a	chr3:156536612-156536621
32	FOS	chr3:156536629-156537126	MCF10A-Er-Src	breast:	n/a	chr3:156536937-156536948
33	FOSL2	chr3:156536600-156537215	SK-N-SH	brain:	n/a	chr3:156536612-156536621
34	POLR2A	chr3:156536929-156537120	MCF10A-Er-Src	breast:	n/a	n/a
35	TCF12	chr3:156536589-156537150	A549	lung:	n/a	n/a
36	JUND	chr3:156536673-156537251	HCT-116	colon:	n/a	n/a
37	GATA3	chr3:156536634-156537141	MCF-7	breast:	n/a	n/a
38	MYC	chr3:156536668-156537197	MCF10A-Er-Src	breast:	n/a	n/a
39	MAX	chr3:156536596-156537220	HCT-116	colon:	n/a	n/a
40	POLR2A	chr3:156536641-156537129	Hela-S3	cervix:	n/a	n/a
41	FOS	chr3:156536740-156537120	Hela-S3	cervix:	n/a	chr3:156536937-156536948
42	JUN	chr3:156536763-156537137	K562	blood:	n/a	n/a

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	chr3:156533566..156537799-chr3:156875553..156879495,5	MCF-7	breast:
8	chr3:156389670..156395497-chr3:156530360..156537244,22	MCF-7	breast:

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

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10513495	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12636629	0.92[EUR][1000 genomes]
rs1367312	0.81[CEU][hapmap];0.90[EUR][1000 genomes]
rs1529581	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17373227	0.88[EUR][1000 genomes]
rs344004	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs41366145	0.92[EUR][1000 genomes]
rs4364127	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55686038	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56128116	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56152727	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56245561	0.87[EUR][1000 genomes]
rs56354026	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56357051	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56836190	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56960846	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57483705	0.92[EUR][1000 genomes]
rs58263861	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58822703	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59689193	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60032002	0.82[ASN][1000 genomes]
rs60178381	1.00[ASN][1000 genomes]
rs73013957	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73019737	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73019748	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73019749	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs891463	0.81[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs919520	LINC00886	cis	Artery Tibial	GTEx
rs919520	LINC00886	cis	Heart Left Ventricle	GTEx
rs919520	LINC00886	cis	Thyroid	GTEx
rs919520	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156535000-156537200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:156535400-156537200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:156535400-156538800	Weak transcription	Lung	lung
4	chr3:156535400-156539000	Enhancers	HSMM	muscle
5	chr3:156535400-156539200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:156535400-156543400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:156535600-156537200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:156535600-156537200	Enhancers	Duodenum Mucosa	Duodenum
9	chr3:156535600-156538000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:156535600-156538600	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr3:156535600-156538600	Enhancers	NHLF	lung
12	chr3:156535600-156538800	Enhancers	HSMMtube	muscle
13	chr3:156535600-156538800	Enhancers	NHDF-Ad	bronchial
14	chr3:156535600-156539000	Enhancers	HMEC	breast
15	chr3:156535600-156539000	Enhancers	HUVEC	blood vessel
16	chr3:156535800-156537600	Enhancers	K562	blood
17	chr3:156535800-156537800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:156536200-156537200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:156536200-156538000	Weak transcription	Stomach Mucosa	stomach
20	chr3:156536200-156538800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:156536200-156539000	Enhancers	Muscle Satellite Cultured Cells	--
22	chr3:156536200-156543200	Weak transcription	Fetal Kidney	kidney
23	chr3:156536400-156538800	Enhancers	NHEK	skin
24	chr3:156536400-156539000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:156536400-156539000	Enhancers	Hela-S3	cervix
26	chr3:156536400-156539000	Enhancers	Osteobl	bone
27	chr3:156536400-156542400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr3:156536400-156542400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:156536400-156543000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:156536400-156543200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:156536400-156543200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr3:156536400-156543200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr3:156536400-156543200	Weak transcription	Thymus	Thymus
34	chr3:156536600-156537600	Flanking Active TSS	A549	lung
35	chr3:156536600-156541600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:156536800-156541800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:156537000-156537400	Enhancers	GM12878-XiMat	blood
38	chr3:156537000-156537400	Enhancers	HepG2	liver
39	chr3:156537000-156539000	Enhancers	NH-A	brain
40	chr3:156537000-156540400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:156537000-156540400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:156537000-156541800	Weak transcription	Fetal Intestine Small	intestine
43	chr3:156537000-156543200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:156537000-156543400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:156537000-156543400	Weak transcription	Liver	Liver
46	chr3:156537000-156543600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr3:156537000-156543600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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