Variant report

Variant	rs11630347
Chromosome Location	chr15:62352843-62352844
allele	A/C/G/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	CTCF	chr15:62352552-62353031	H1-hESC	embryonic stem cell:	n/a	chr15:62352934-62352952 chr15:62352941-62352949
2	STAT3	chr15:62352730-62352921	MCF10A-Er-Src	breast:	n/a	n/a
3	CREB1	chr15:62351897-62353034	GM12878	blood:	n/a	n/a
4	CHD1	chr15:62351725-62353087	GM12878	blood:	n/a	n/a
5	RAD21	chr15:62352484-62353092	A549	lung:	n/a	chr15:62352621-62352634
6	SPI1	chr15:62352657-62352951	GM12878	blood:	n/a	n/a
7	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
8	ZBTB7A	chr15:62352165-62352938	ECC-1	luminal epithelium:	n/a	n/a
9	ZNF143	chr15:62352090-62352961	Hela-S3	cervix:	n/a	chr15:62352375-62352385 chr15:62352614-62352624
10	YY1	chr15:62352323-62352885	K562	blood:	n/a	chr15:62352425-62352439 chr15:62352454-62352468 chr15:62352375-62352389
11	E2F4	chr15:62352735-62353072	GM12878	blood:	n/a	chr15:62352929-62352936 chr15:62352928-62352940 chr15:62352929-62352936 chr15:62352929-62352936
12	POLR2A	chr15:62351927-62353148	H1-neurons	neurons:	n/a	n/a
13	CTCF	chr15:62352700-62352850	K562	blood:	n/a	n/a
14	BRCA1	chr15:62352445-62353047	H1-hESC	embryonic stem cell:	n/a	n/a
15	EP300	chr15:62352110-62353099	HepG2	liver:	n/a	n/a
16	POLR2A	chr15:62351995-62353047	ECC-1	luminal epithelium:	n/a	n/a
17	CTCF	chr15:62352514-62353055	A549	lung:	n/a	chr15:62352934-62352952 chr15:62352941-62352949
18	RAD21	chr15:62352458-62352970	IMR90	lung:	n/a	chr15:62352621-62352634
19	CTCF	chr15:62352504-62353100	Fibrobl	skin:	n/a	chr15:62352934-62352952 chr15:62352941-62352949
20	UBTF	chr15:62351765-62353080	K562	blood:	n/a	n/a
21	CTCF	chr15:62352720-62352870	HepG2	liver:	n/a	n/a
22	NR2F2	chr15:62352448-62353042	MCF-7	breast:	n/a	n/a
23	SIN3AK20	chr15:62352482-62353045	A549	lung:	n/a	n/a
24	CTCF	chr15:62352740-62352890	HAc	cerebellar:	n/a	n/a
25	CTCF	chr15:62352720-62352870	HBMEC	blood vessel:	n/a	n/a
26	ELK1	chr15:62352032-62352931	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr15:62352663-62352921	GM13977	blood:	n/a	n/a
28	CTCF	chr15:62352652-62352957	K562	blood:	n/a	chr15:62352934-62352952 chr15:62352941-62352949
29	TRIM28	chr15:62352508-62353013	K562	blood:	n/a	n/a
30	POLR2A	chr15:62352139-62353068	MCF-7	breast:	n/a	n/a
31	ELK1	chr15:62352480-62352920	K562	blood:	n/a	n/a
32	HEY1	chr15:62352431-62352892	HepG2	liver:	n/a	chr15:62352710-62352725 chr15:62352696-62352711 chr15:62352444-62352459
33	TCF7L2	chr15:62351997-62353327	Hela-S3	cervix:	n/a	n/a
34	NRF1	chr15:62352549-62352867	HepG2	liver:	n/a	chr15:62352704-62352713 chr15:62352704-62352718 chr15:62352663-62352674 chr15:62352703-62352714 chr15:62352704-62352715 chr15:62352701-62352715 chr15:62352681-62352690
35	TFAP2C	chr15:62351925-62353048	Hela-S3	cervix:	n/a	chr15:62352219-62352234
36	TCF7L2	chr15:62352077-62353360	PANC-1	pancreas:	n/a	n/a
37	CTCF	chr15:62352740-62352890	AG04450	lung:	n/a	n/a
38	CREB1	chr15:62352448-62353060	H1-hESC	embryonic stem cell:	n/a	n/a
39	TBP	chr15:62352457-62352937	HepG2	liver:	n/a	n/a
40	MAX	chr15:62352395-62353101	MCF-7	breast:	n/a	n/a
41	POLR2A	chr15:62352321-62352848	ECC-1	luminal epithelium:	n/a	n/a
42	RCOR1	chr15:62351272-62352990	Hela-S3	cervix:	n/a	n/a
43	USF1	chr15:62352455-62352937	SK-N-SH_RA	brain:	n/a	n/a
44	TAF1	chr15:62352430-62352889	Hela-S3	cervix:	n/a	n/a
45	TBP	chr15:62352063-62353048	H1-hESC	embryonic stem cell:	n/a	n/a
46	RAD21	chr15:62352522-62352960	SK-N-SH_RA	brain:	n/a	chr15:62352621-62352634
47	ZNF143	chr15:62352366-62353058	K562	blood:	n/a	chr15:62352375-62352385 chr15:62352614-62352624
48	MAFK	chr15:62352591-62353009	K562	blood:	n/a	n/a
49	CTCF	chr15:62352486-62353043	A549	lung:	n/a	chr15:62352934-62352952 chr15:62352941-62352949
50	CTCF	chr15:62352740-62352890	BE2_C	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:62352827-62352877	Hela-S3	cervix:	n/a
2	chr15:62352827-62352877	NH-A	brain:	n/a
3	chr15:62352810-62352860	SK-N-SH	brain:	n/a
4	chr15:62352810-62352860	PANC-1	pancreas:	n/a
5	chr15:62352810-62352860	ECC-1	luminal epithelium:	n/a
6	chr15:62352827-62352877	HCF	heart:	n/a
7	chr15:62352810-62352860	T-47D	breast:	n/a
8	chr15:62352810-62352860	AG09309	skin:	n/a
9	chr15:62352810-62352860	K562	blood:	n/a
10	chr15:62352810-62352860	SK-N-SH_RA	brain:	n/a
11	chr15:62352827-62352877	H1-hESC	embryonic stem cell:	embryo
12	chr15:62352836-62352886	LNCaP	prostate:	n/a
13	chr15:62352836-62352886	HEK293	kidney:	embryo
14	chr15:62352827-62352877	GM06990	blood:	n/a
15	chr15:62352836-62352886	HMEC	breast:	n/a
16	chr15:62352836-62352886	AG10803	skin:	n/a
17	chr15:62352810-62352860	CMK	blood:	n/a
18	chr15:62352810-62352860	U87	brain:	n/a
19	chr15:62352836-62352886	HCF	heart:	n/a
20	chr15:62352836-62352886	SK-N-SH_RA	brain:	n/a
21	chr15:62352827-62352877	PFSK-1	brain:	n/a
22	chr15:62352836-62352886	HepG2	liver:	n/a
23	chr15:62352827-62352877	HPAEpiC	pulmonary alveolar:	n/a
24	chr15:62352810-62352860	HL-60	blood:	n/a
25	chr15:62352836-62352886	NHDF-neo	bronchial:	n/a
26	chr15:62352836-62352886	Caco-2	colon:	n/a
27	chr15:62352810-62352860	HRPEpiC	eye:	n/a
28	chr15:62352827-62352877	HRE	kidney:	n/a
29	chr15:62352836-62352886	NB4	blood:	n/a
30	chr15:62352836-62352886	SKMC	muscle:	n/a
31	chr15:62352810-62352860	HAEpiC	amniotic membrane:	n/a
32	chr15:62352810-62352860	HRCEpiC	kidney:	n/a
33	chr15:62352836-62352886	A549	lung:	n/a
34	chr15:62352810-62352860	SKMC	muscle:	n/a
35	chr15:62352810-62352860	BE2_C	brain:	n/a
36	chr15:62352810-62352860	Jurkat	blood:	n/a
37	chr15:62352836-62352886	T-47D	breast:	n/a
38	chr15:62352810-62352860	NH-A	brain:	n/a
39	chr15:62352827-62352877	SK-N-MC	brain:	n/a
40	chr15:62352827-62352877	HCT-116	colon:	n/a
41	chr15:62352836-62352886	GM06990	blood:	n/a
42	chr15:62352810-62352860	HCM	heart:	n/a
43	chr15:62352836-62352886	PrEC	prostate:	n/a
44	chr15:62352836-62352886	RPTEC	kidney:	n/a
45	chr15:62352827-62352877	PANC-1	pancreas:	n/a
46	chr15:62352836-62352886	Jurkat	blood:	n/a
47	chr15:62352810-62352860	HEK293	kidney:	embryo
48	chr15:62352810-62352860	MCF-7	breast:	n/a
49	chr15:62352827-62352877	GM19239	blood:	n/a
50	chr15:62352810-62352860	A549	lung:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:62283890..62286224-chr15:62350363..62353063,2	K562	blood:
2	chr12:7052550..7053303-chr15:62352155..62353139,2	HCT-116	colon:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C2CD4A-1	chr15:62352738-62353042	XLOC_011278
2	lnc-C2CD4A-1	chr15:62352713-62354633	ENSG00000259251.2
3	lnc-C2CD4A-1	chr15:62352702-62353042	ENSG00000259251.2

Variant related genes	Relation type
VPS13C	TF binding region
VPS13C	CpG island
ENSG00000111678	Chromatin interaction
ENSG00000238923	Chromatin interaction
ENSG00000129003	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1030860	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1030861	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10468027	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10519153	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10851704	0.81[AMR][1000 genomes]
rs10851707	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11071647	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11071648	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11071650	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11629528	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11632441	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11632842	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11634693	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11635621	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11639147	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442589	0.90[EUR][1000 genomes]
rs12443311	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12592464	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12593844	0.87[ASN][1000 genomes]
rs12595300	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12898209	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12899801	0.87[ASN][1000 genomes]
rs12900703	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12901575	0.91[AMR][1000 genomes];0.85[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]
rs12917535	0.81[AMR][1000 genomes]
rs1364810	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1370177	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1436961	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1436965	0.87[AMR][1000 genomes]
rs1436966	0.98[ASN][1000 genomes]
rs1534542	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1561197	0.86[AMR][1000 genomes]
rs1836996	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2042610	0.82[AMR][1000 genomes]
rs2414756	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2414758	0.83[AMR][1000 genomes]
rs2414759	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2899678	0.87[AMR][1000 genomes]
rs3743294	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3784445	0.82[EUR][1000 genomes]
rs4143841	0.82[EUR][1000 genomes]
rs4372632	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4638519	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7161883	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7168164	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8023668	0.87[AMR][1000 genomes]
rs8029942	0.98[ASN][1000 genomes]
rs8033816	0.86[ASN][1000 genomes]
rs9635310	0.81[EUR][1000 genomes]
rs9989353	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9989354	0.91[AMR][1000 genomes];0.94[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	chr15:62351000-62353600	Active TSS	Right Atrium	heart
4	chr15:62351000-62353800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:62351200-62353000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr15:62351200-62353400	Active TSS	NHLF	lung
7	chr15:62351200-62353800	Active TSS	GM12878-XiMat	blood
8	chr15:62351400-62353000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:62351400-62353000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr15:62351400-62353000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr15:62351400-62353000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:62351400-62353000	Active TSS	HepG2	liver
13	chr15:62351400-62353200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr15:62351400-62353200	Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr15:62351400-62353200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr15:62351400-62353200	Active TSS	HSMM	muscle
17	chr15:62351400-62353400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr15:62351400-62353400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
19	chr15:62351400-62353400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:62351400-62353400	Active TSS	Colonic Mucosa	Colon
21	chr15:62351400-62353400	Active TSS	Fetal Brain Female	brain
22	chr15:62351400-62353400	Active TSS	Psoas Muscle	Psoas
23	chr15:62351400-62353400	Active TSS	A549	lung
24	chr15:62351400-62353600	Active TSS	Aorta	Aorta
25	chr15:62351400-62353600	Active TSS	Fetal Brain Male	brain
26	chr15:62351400-62353600	Active TSS	HSMMtube	muscle
27	chr15:62351400-62353800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:62351400-62354000	Active TSS	Primary T cells fromperipheralblood	blood
29	chr15:62351600-62353000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:62351600-62353000	Active TSS	Fetal Muscle Trunk	muscle
31	chr15:62351600-62353200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:62351600-62353200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:62351600-62353200	Active TSS	Fetal Intestine Large	intestine
34	chr15:62351600-62353200	Active TSS	Fetal Intestine Small	intestine
35	chr15:62351600-62353200	Active TSS	Placenta	Placenta
36	chr15:62351600-62353400	Active TSS	Fetal Kidney	kidney
37	chr15:62351600-62353400	Active TSS	Right Ventricle	heart
38	chr15:62351600-62353400	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr15:62351600-62353400	Active TSS	Small Intestine	intestine
40	chr15:62351600-62353400	Active TSS	Stomach Mucosa	stomach
41	chr15:62351600-62353600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
42	chr15:62351600-62353600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr15:62351600-62353600	Active TSS	Brain Cingulate Gyrus	brain
44	chr15:62351600-62353600	Active TSS	Brain Hippocampus Middle	brain
45	chr15:62351600-62353600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr15:62351600-62353600	Active TSS	Colon Smooth Muscle	Colon
47	chr15:62351600-62353600	Active TSS	Fetal Thymus	thymus
48	chr15:62351600-62353800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr15:62351600-62353800	Active TSS	Brain Substantia Nigra	brain
50	chr15:62351600-62353800	Active TSS	Ovary	ovary

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