Variant report

Variant	rs953159
Chromosome Location	chr15:50648711-50648712
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:30)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:43 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:50645890-50649461	GM18505	blood:	n/a	n/a
2	POLR2A	chr15:50643941-50650733	GM12891	blood:	n/a	n/a
3	POLR2A	chr15:50648646-50650254	GM12892	blood:	n/a	n/a
4	POLR2A	chr15:50645476-50650223	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:50646827-50649588	HepG2	liver:	n/a	n/a
6	POLR2A	chr15:50645950-50649548	K562	blood:	n/a	n/a
7	MTA3	chr15:50645838-50649091	GM12878	blood:	n/a	n/a
8	POLR2A	chr15:50648364-50648923	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr15:50643964-50649543	GM12878	blood:	n/a	n/a
10	POLR2A	chr15:50645530-50650223	K562	blood:	n/a	n/a
11	POLR2A	chr15:50648531-50650361	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr15:50648641-50649498	GM12891	blood:	n/a	n/a
13	POLR2A	chr15:50645808-50650538	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr15:50645780-50648825	GM12892	blood:	n/a	n/a
15	POLR2A	chr15:50645464-50650252	K562	blood:	n/a	n/a
16	POLR2A	chr15:50645959-50649428	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr15:50646787-50650247	K562	blood:	n/a	n/a
18	MYC	chr15:50645294-50648723	A549	lung:	n/a	chr15:50646903-50646913 chr15:50647687-50647697 chr15:50645298-50645305
19	CHD1	chr15:50645756-50648859	H1-hESC	embryonic stem cell:	n/a	chr15:50647640-50647650 chr15:50646931-50646941
20	POLR2A	chr15:50648648-50650323	SK-N-MC	brain:	n/a	n/a
21	CHD1	chr15:50645052-50649822	IMR90	lung:	n/a	chr15:50647640-50647650 chr15:50646931-50646941
22	POLR2A	chr15:50648702-50650294	MCF-7	breast:	n/a	n/a
23	POLR2A	chr15:50645917-50648744	K562	blood:	n/a	n/a
24	POLR2A	chr15:50648563-50649654	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr15:50645847-50649076	HepG2	liver:	n/a	n/a
26	POLR2A	chr15:50648710-50650269	GM12878	blood:	n/a	n/a
27	MXI1	chr15:50644670-50649694	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr15:50645929-50649031	ProgFib	skin:	n/a	n/a
29	POLR2A	chr15:50643912-50651678	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr15:50648611-50648933	HCT-116	colon:	n/a	n/a
31	POLR2A	chr15:50643981-50656245	MCF10A-Er-Src	breast:	n/a	n/a
32	RFX5	chr15:50648230-50648835	K562	blood:	n/a	n/a
33	POLR2A	chr15:50644647-50648996	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr15:50648495-50649703	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr15:50646088-50651672	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr15:50645894-50648777	Hela-S3	cervix:	n/a	n/a
37	HCFC1	chr15:50645295-50649087	Hela-S3	cervix:	n/a	n/a
38	GABPA	chr15:50645600-50648796	MCF-7	breast:	n/a	chr15:50647647-50647661 chr15:50647650-50647661 chr15:50647652-50647661 chr15:50647371-50647380
39	POLR2A	chr15:50646019-50649543	PANC-1	pancreas:	n/a	n/a
40	POLR2A	chr15:50644838-50649712	IMR90	lung:	n/a	n/a
41	POLR2A	chr15:50648627-50649455	GM12892	blood:	n/a	n/a
42	POLR2A	chr15:50645312-50650230	GM12878	blood:	n/a	n/a
43	MYC	chr15:50646908-50649003	MCF10A-Er-Src	breast:	n/a	chr15:50647687-50647697

No data

(count:30 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:50645594..50649830-chr15:50754186..50757976,9	MCF-7	breast:
2	chr15:50646435..50649191-chr15:52859384..52862079,2	MCF-7	breast:
3	chr15:50473235..50476211-chr15:50645559..50648841,7	MCF-7	breast:
4	chr15:50643045..50650563-chr15:50756489..50761004,9	MCF-7	breast:
5	chr15:50647013..50649194-chr15:51198882..51202798,3	K562	blood:
6	chr15:50471646..50476620-chr15:50646050..50650091,9	MCF-7	breast:
7	chr15:50647163..50649970-chr15:50707470..50713022,5	MCF-7	breast:
8	chr15:50644389..50649393-chr15:50787180..50791359,7	MCF-7	breast:
9	chr15:50646264..50649073-chr17:62500886..62503658,2	MCF-7	breast:
10	chr15:50645553..50650972-chr15:51199033..51203961,11	MCF-7	breast:
11	chr15:50647220..50649637-chr15:50708002..50709799,2	K562	blood:
12	chr15:50513432..50516110-chr15:50646563..50649335,2	MCF-7	breast:
13	chr15:50552898..50556236-chr15:50646166..50649137,4	K562	blood:
14	chr11:66486776..66489307-chr15:50646648..50649417,2	MCF-7	breast:
15	chr15:50644809..50652796-chr15:50713240..50720627,20	K562	blood:
16	chr15:50646198..50649019-chr15:50789771..50791870,3	MCF-7	breast:
17	chr15:50645588..50649349-chr15:50728196..50732461,4	MCF-7	breast:
18	chr15:50646468..50650762-chr15:50786083..50789645,4	K562	blood:
19	chr15:50646359..50649336-chr15:50872616..50874692,3	MCF-7	breast:
20	chr15:50644978..50654282-chr15:50714279..50723145,48	MCF-7	breast:
21	chr15:50645261..50648746-chr15:51197475..51202828,11	MCF-7	breast:
22	chr15:50646763..50649574-chr8:128746981..128748587,2	MCF-7	breast:
23	chr15:50644601..50650486-chr15:50714318..50720349,10	K562	blood:
24	chr15:50644770..50653815-chr15:50713287..50720249,51	MCF-7	breast:
25	chr15:50481284..50485703-chr15:50645023..50648855,4	MCF-7	breast:
26	chr15:50646196..50649637-chr15:50705519..50710625,4	K562	blood:
27	chr15:50647970..50649936-chr15:50757455..50759138,2	K562	blood:
28	chr15:50648117..50650493-chr15:50779482..50782033,2	K562	blood:
29	chr15:50647443..50649396-chr15:50783549..50786868,3	MCF-7	breast:
30	chr11:20407767..20409374-chr15:50647141..50649461,2	MCF-7	breast:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USP8-2	chr15:50648297-50650501	ENSG00000244879
2	lnc-USP8-2	chr15:50648668-50649115	ENSG00000244879.2
3	lnc-USP8-2	chr15:50646371-50650503	NONHSAT042406
4	lnc-USP8-2	chr15:50648297-50650501	NONHSAT042411
5	lnc-USP8-2	chr15:50648297-50650527	ENSG00000244879.2

No data

Variant related genes	Relation type
MIR4712	TF binding region
GABPB1	TF binding region
ENSG00000092439	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000138592	Chromatin interaction
ENSG00000104043	Chromatin interaction
ENSG00000140284	Chromatin interaction
ENSG00000259298	Chromatin interaction
ENSG00000081014	Chromatin interaction
ENSG00000140287	Chromatin interaction
ENSG00000173898	Chromatin interaction
ENSG00000128989	Chromatin interaction
ENSG00000200605	Chromatin interaction
ENSG00000136997	Chromatin interaction
ENSG00000259618	Chromatin interaction
ENSG00000185238	Chromatin interaction
ENSG00000258890	Chromatin interaction
ENSG00000259465	Chromatin interaction
ENSG00000252376	Chromatin interaction
ENSG00000242737	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10083714	0.82[ASN][1000 genomes]
rs10152574	0.92[ASN][1000 genomes]
rs11491094	0.82[ASN][1000 genomes]
rs16963562	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs16963571	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16963573	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16963578	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16963582	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16963638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1896169	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1955101	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs55697237	0.92[ASN][1000 genomes]
rs55774471	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55950921	0.92[ASN][1000 genomes]
rs56812974	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58903525	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59847008	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60893904	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs717025	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7177488	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74012326	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74012336	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74012366	0.92[ASN][1000 genomes]
rs74012367	0.92[ASN][1000 genomes]
rs8028745	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8029259	0.82[ASN][1000 genomes]
rs8029439	0.82[ASN][1000 genomes]
rs8034492	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8040420	0.86[ASN][1000 genomes]
rs8040483	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9652452	0.82[ASN][1000 genomes]

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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
4	nsv948579	chr15:50645530-51045564	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50644200-50648800	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr15:50644400-50648800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:50644400-50649000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr15:50644400-50649200	Active TSS	Fetal Brain Female	brain
5	chr15:50644400-50649400	Active TSS	NHLF	lung
6	chr15:50644600-50648800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr15:50644600-50649200	Active TSS	H1 Cell Line	embryonic stem cell
8	chr15:50644600-50649200	Active TSS	GM12878-XiMat	blood
9	chr15:50644600-50649800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:50644800-50648800	Active TSS	Thymus	Thymus
11	chr15:50644800-50649200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr15:50644800-50649200	Active TSS	Right Ventricle	heart
13	chr15:50645000-50648800	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr15:50645000-50649000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:50645000-50649000	Active TSS	Primary T cells fromperipheralblood	blood
16	chr15:50645000-50649000	Active TSS	Fetal Muscle Leg	muscle
17	chr15:50645000-50649000	Active TSS	NHDF-Ad	bronchial
18	chr15:50645000-50649200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:50645000-50649200	Active TSS	Fetal Thymus	thymus
20	chr15:50645000-50649600	Active TSS	Psoas Muscle	Psoas
21	chr15:50645200-50649000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:50645400-50648800	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr15:50645400-50649400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr15:50645600-50648800	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr15:50645600-50649000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:50645600-50649600	Active TSS	H9 Cell Line	embryonic stem cell
27	chr15:50645800-50648800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr15:50645800-50648800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr15:50647000-50648800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:50647000-50649400	Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr15:50647200-50648800	Active TSS	Fetal Brain Male	brain
32	chr15:50647200-50649000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:50647400-50649200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:50647600-50649000	Active TSS	Brain Germinal Matrix	brain
35	chr15:50647800-50649000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr15:50647800-50649000	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr15:50647800-50649000	Active TSS	Right Atrium	heart
38	chr15:50647800-50649200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr15:50647800-50649400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr15:50647800-50649600	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr15:50647800-50649600	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr15:50647800-50649600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr15:50647800-50649600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:50647800-50649800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:50648000-50648800	Active TSS	HepG2	liver
46	chr15:50648000-50649000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:50648000-50649000	Flanking Active TSS	Liver	Liver
48	chr15:50648000-50649000	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr15:50648000-50649000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
50	chr15:50648000-50649000	Weak transcription	Gastric	stomach

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