Variant report

Variant	rs11639147
Chromosome Location	chr15:62352374-62352375
allele	A/G
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	CREB1	chr15:62351897-62353034	GM12878	blood:	n/a	n/a
2	CHD1	chr15:62351725-62353087	GM12878	blood:	n/a	n/a
3	IRF1	chr15:62351724-62353018	K562	blood:	n/a	chr15:62352108-62352128 chr15:62352113-62352127 chr15:62352116-62352126 chr15:62352108-62352121 chr15:62352108-62352121 chr15:62352108-62352121 chr15:62352112-62352126
4	ZBTB7A	chr15:62352165-62352938	ECC-1	luminal epithelium:	n/a	n/a
5	ZNF143	chr15:62352090-62352961	Hela-S3	cervix:	n/a	chr15:62352375-62352385 chr15:62352614-62352624
6	YY1	chr15:62352323-62352885	K562	blood:	n/a	chr15:62352425-62352439 chr15:62352454-62352468 chr15:62352375-62352389
7	POLR2A	chr15:62351927-62353148	H1-neurons	neurons:	n/a	n/a
8	EP300	chr15:62352110-62353099	HepG2	liver:	n/a	n/a
9	POLR2A	chr15:62351995-62353047	ECC-1	luminal epithelium:	n/a	n/a
10	UBTF	chr15:62351765-62353080	K562	blood:	n/a	n/a
11	ELK1	chr15:62352032-62352931	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr15:62352139-62353068	MCF-7	breast:	n/a	n/a
13	TCF7L2	chr15:62351997-62353327	Hela-S3	cervix:	n/a	n/a
14	TFAP2C	chr15:62351925-62353048	Hela-S3	cervix:	n/a	chr15:62352219-62352234
15	TCF7L2	chr15:62352077-62353360	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr15:62352321-62352848	ECC-1	luminal epithelium:	n/a	n/a
17	RCOR1	chr15:62351272-62352990	Hela-S3	cervix:	n/a	n/a
18	TBP	chr15:62352063-62353048	H1-hESC	embryonic stem cell:	n/a	n/a
19	ZNF143	chr15:62352366-62353058	K562	blood:	n/a	chr15:62352375-62352385 chr15:62352614-62352624
20	POLR2A	chr15:62352277-62352815	K562	blood:	n/a	n/a
21	CHD2	chr15:62351850-62353366	GM12878	blood:	n/a	n/a
22	POLR2A	chr15:62352077-62353044	Gliobla	brain:	n/a	n/a
23	POLR2A	chr15:62351783-62352812	GM12892	blood:	n/a	n/a
24	UBTF	chr15:62351815-62353083	K562	blood:	n/a	n/a
25	TAF1	chr15:62352091-62352969	ECC-1	luminal epithelium:	n/a	n/a
26	JUND	chr15:62351576-62353024	K562	blood:	n/a	n/a
27	ELF1	chr15:62351877-62353153	GM12878	blood:	n/a	chr15:62352042-62352055 chr15:62352044-62352055 chr15:62352388-62352400 chr15:62352612-62352624
28	YY1	chr15:62351868-62353083	GM12878	blood:	n/a	chr15:62352425-62352439 chr15:62352454-62352468 chr15:62352254-62352268 chr15:62352375-62352389
29	POLR2A	chr15:62351914-62353381	GM19193	blood:	n/a	n/a
30	MAX	chr15:62351821-62353215	A549	lung:	n/a	n/a
31	POLR2A	chr15:62351815-62352962	GM12878	blood:	n/a	n/a
32	WRNIP1	chr15:62351824-62353304	GM12878	blood:	n/a	n/a
33	POLR2A	chr15:62351872-62352913	GM12878	blood:	n/a	n/a
34	YY1	chr15:62351910-62353002	GM12892	blood:	n/a	chr15:62352425-62352439 chr15:62352454-62352468 chr15:62352254-62352268 chr15:62352375-62352389
35	ZMIZ1	chr15:62352268-62352992	K562	blood:	n/a	n/a
36	TBP	chr15:62351636-62352935	GM12878	blood:	n/a	n/a
37	EBF1	chr15:62351893-62352398	GM12878	blood:	n/a	n/a
38	MAX	chr15:62351849-62353320	HCT-116	colon:	n/a	n/a
39	MXI1	chr15:62351331-62353306	IMR90	lung:	n/a	chr15:62353005-62353020
40	BCLAF1	chr15:62352347-62353138	GM12878	blood:	n/a	chr15:62352695-62352708 chr15:62352436-62352449
41	MAX	chr15:62351929-62353189	H1-hESC	embryonic stem cell:	n/a	n/a
42	HEY1	chr15:62352354-62352807	K562	blood:	n/a	chr15:62352710-62352725 chr15:62352696-62352711 chr15:62352444-62352459
43	CHD2	chr15:62352007-62353086	H1-hESC	embryonic stem cell:	n/a	n/a
44	USF2	chr15:62352062-62353062	GM12878	blood:	n/a	chr15:62352932-62352948 chr15:62352966-62352982
45	SIN3A	chr15:62351893-62353247	GM12878	blood:	n/a	chr15:62352436-62352445 chr15:62352620-62352631
46	NFIC	chr15:62351788-62353409	GM12878	blood:	n/a	n/a
47	STAT5A	chr15:62351887-62353013	GM12878	blood:	n/a	chr15:62352192-62352204
48	POLR2A	chr15:62351729-62352902	GM12878	blood:	n/a	n/a
49	TAF1	chr15:62351934-62352868	H1-neurons	neurons:	n/a	n/a
50	RCOR1	chr15:62351813-62353472	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:62351924..62352564-chr19:13953304..13953928,2	NB4	blood:
2	chr15:62346399..62348627-chr15:62350177..62352518,4	MCF-7	breast:
3	chr15:62283890..62286224-chr15:62350363..62353063,2	K562	blood:
4	chr12:7052550..7053303-chr15:62352155..62353139,2	HCT-116	colon:

Variant related genes	Relation type
ENSG00000259251	TF binding region
ENSG00000111678	Chromatin interaction
ENSG00000129003	Chromatin interaction
ENSG00000238923	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1030860	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1030861	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10468027	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10519153	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10851707	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11071647	0.80[EUR][1000 genomes]
rs11071648	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11071650	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11629528	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11630347	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632441	0.86[EUR][1000 genomes]
rs11632842	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11634693	0.83[EUR][1000 genomes]
rs11635621	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12442589	0.91[EUR][1000 genomes]
rs12443311	0.81[EUR][1000 genomes]
rs12592464	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12593844	0.87[ASN][1000 genomes]
rs12595300	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12898209	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12899801	0.87[ASN][1000 genomes]
rs12900703	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12901575	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12909947	0.86[ASN][1000 genomes]
rs12910541	0.86[ASN][1000 genomes]
rs12912208	0.98[ASN][1000 genomes]
rs1364810	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1370177	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1436961	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1436965	0.83[AMR][1000 genomes]
rs1436966	0.98[ASN][1000 genomes]
rs1534542	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1561197	0.83[AMR][1000 genomes]
rs1836996	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2414756	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2414759	0.86[EUR][1000 genomes]
rs2899678	0.84[AMR][1000 genomes]
rs3743294	0.82[EUR][1000 genomes]
rs3784445	0.81[EUR][1000 genomes]
rs4143841	0.82[EUR][1000 genomes]
rs4372632	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4638519	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7161883	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7168164	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8023668	0.84[AMR][1000 genomes]
rs8029942	0.98[ASN][1000 genomes]
rs8033816	0.86[ASN][1000 genomes]
rs9635310	0.82[EUR][1000 genomes]
rs9989353	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9989354	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904288	chr15:62146598-62356386	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv904290	chr15:62175134-62356386	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv904294	chr15:62178695-62356386	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv457176	chr15:62178695-62519658	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv569643	chr15:62178695-62519658	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv471247	chr15:62202481-62519658	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv569646	chr15:62202482-62519658	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1044748	chr15:62276183-62521856	Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv542405	chr15:62276183-62521856	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv457178	chr15:62340126-62394324	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv569652	chr15:62340126-62394324	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62350400-62353000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:62350800-62353600	Active TSS	NHDF-Ad	bronchial
3	chr15:62351000-62352800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:62351000-62353600	Active TSS	Right Atrium	heart
5	chr15:62351000-62353800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:62351200-62353000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:62351200-62353400	Active TSS	NHLF	lung
8	chr15:62351200-62353800	Active TSS	GM12878-XiMat	blood
9	chr15:62351400-62353000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:62351400-62353000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr15:62351400-62353000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:62351400-62353000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
13	chr15:62351400-62353000	Active TSS	HepG2	liver
14	chr15:62351400-62353200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr15:62351400-62353200	Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr15:62351400-62353200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:62351400-62353200	Active TSS	HSMM	muscle
18	chr15:62351400-62353400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:62351400-62353400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr15:62351400-62353400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:62351400-62353400	Active TSS	Colonic Mucosa	Colon
22	chr15:62351400-62353400	Active TSS	Fetal Brain Female	brain
23	chr15:62351400-62353400	Active TSS	Psoas Muscle	Psoas
24	chr15:62351400-62353400	Active TSS	A549	lung
25	chr15:62351400-62353600	Active TSS	Aorta	Aorta
26	chr15:62351400-62353600	Active TSS	Fetal Brain Male	brain
27	chr15:62351400-62353600	Active TSS	HSMMtube	muscle
28	chr15:62351400-62353800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr15:62351400-62354000	Active TSS	Primary T cells fromperipheralblood	blood
30	chr15:62351600-62352800	Active TSS	Fetal Stomach	stomach
31	chr15:62351600-62352800	Active TSS	HMEC	breast
32	chr15:62351600-62353000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:62351600-62353000	Active TSS	Fetal Muscle Trunk	muscle
34	chr15:62351600-62353200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:62351600-62353200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:62351600-62353200	Active TSS	Fetal Intestine Large	intestine
37	chr15:62351600-62353200	Active TSS	Fetal Intestine Small	intestine
38	chr15:62351600-62353200	Active TSS	Placenta	Placenta
39	chr15:62351600-62353400	Active TSS	Fetal Kidney	kidney
40	chr15:62351600-62353400	Active TSS	Right Ventricle	heart
41	chr15:62351600-62353400	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr15:62351600-62353400	Active TSS	Small Intestine	intestine
43	chr15:62351600-62353400	Active TSS	Stomach Mucosa	stomach
44	chr15:62351600-62353600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
45	chr15:62351600-62353600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr15:62351600-62353600	Active TSS	Brain Cingulate Gyrus	brain
47	chr15:62351600-62353600	Active TSS	Brain Hippocampus Middle	brain
48	chr15:62351600-62353600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr15:62351600-62353600	Active TSS	Colon Smooth Muscle	Colon
50	chr15:62351600-62353600	Active TSS	Fetal Thymus	thymus

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