Variant report

Variant	rs3751652
Chromosome Location	chr15:40886310-40886311
allele	C/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	TCF7L2	chr15:40885957-40886982	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr15:40885926-40886826	GM12878	blood:	n/a	n/a
3	CEBPB	chr15:40885882-40886399	HepG2	liver:	n/a	n/a
4	STAT5A	chr15:40885804-40886520	K562	blood:	n/a	chr15:40885865-40885873 chr15:40886271-40886283
5	ZNF384	chr15:40885976-40886506	K562	blood:	n/a	n/a
6	POLR2A	chr15:40886043-40886925	H1-hESC	embryonic stem cell:	n/a	n/a
7	REST	chr15:40885925-40886878	HL-60	blood:	n/a	n/a
8	BCLAF1	chr15:40885839-40886609	GM12878	blood:	n/a	chr15:40886393-40886402
9	POLR2A	chr15:40886087-40887052	PBDE	blood:	n/a	n/a
10	HSF1	chr15:40885912-40886739	HepG2	liver:	n/a	n/a
11	TEAD4	chr15:40885953-40886375	MCF-7	breast:	n/a	n/a
12	E2F4	chr15:40886006-40886809	GM12878	blood:	n/a	chr15:40886422-40886431 chr15:40886447-40886456
13	TCF12	chr15:40885947-40886582	GM12878	blood:	n/a	n/a
14	TAF1	chr15:40885898-40886728	PFSK-1	brain:	n/a	n/a
15	GTF3C2	chr15:40885481-40886921	K562	blood:	n/a	n/a
16	TEAD4	chr15:40885694-40886837	K562	blood:	n/a	n/a
17	POLR2A	chr15:40885871-40886723	GM12891	blood:	n/a	n/a
18	RFX5	chr15:40885970-40886520	HepG2	liver:	n/a	n/a
19	PAX5	chr15:40885748-40886419	GM12878	blood:	n/a	n/a
20	RUNX3	chr15:40885812-40887183	GM12878	blood:	n/a	n/a
21	CHD1	chr15:40885809-40887702	IMR90	lung:	n/a	n/a
22	MYC	chr15:40885920-40886420	MCF10A-Er-Src	breast:	n/a	n/a
23	ZNF217	chr15:40885918-40886365	MCF-7	breast:	n/a	n/a
24	ZNF263	chr15:40886041-40887759	HEK293-T-REx	kidney:	n/a	n/a
25	CEBPB	chr15:40885750-40886998	HCT-116	colon:	n/a	n/a
26	POLR2A	chr15:40886103-40886877	HEK293	kidney:	n/a	n/a
27	SMC3	chr15:40885977-40886402	HepG2	liver:	n/a	n/a
28	GABPA	chr15:40885984-40887180	MCF-7	breast:	n/a	chr15:40886421-40886435 chr15:40886423-40886432 chr15:40886421-40886432 chr15:40886418-40886432
29	SIN3AK20	chr15:40886269-40886638	A549	lung:	n/a	n/a
30	SP1	chr15:40885883-40886635	GM12878	blood:	n/a	chr15:40886393-40886402 chr15:40886270-40886279 chr15:40886391-40886403 chr15:40886391-40886403
31	POLR2A	chr15:40885947-40887058	HL-60	blood:	n/a	n/a
32	POLR2A	chr15:40886066-40886896	K562	blood:	n/a	n/a
33	YY1	chr15:40885842-40886660	A549	lung:	n/a	chr15:40886231-40886241 chr15:40886174-40886184 chr15:40886232-40886240 chr15:40886177-40886185 chr15:40886174-40886184 chr15:40886224-40886243 chr15:40886174-40886196
34	CHD2	chr15:40885960-40886440	K562	blood:	n/a	n/a
35	CEBPB	chr15:40885910-40886469	HepG2	liver:	n/a	n/a
36	CEBPB	chr15:40885872-40886387	A549	lung:	n/a	n/a
37	REST	chr15:40885676-40886730	H1-neurons	neurons:	n/a	n/a
38	ETS1	chr15:40885882-40886341	A549	lung:	n/a	n/a
39	NFIC	chr15:40885840-40886682	HepG2	liver:	n/a	chr15:40886323-40886340
40	TBL1XR1	chr15:40885924-40886640	GM12878	blood:	n/a	n/a
41	MAX	chr15:40885936-40887128	ECC-1	luminal epithelium:	n/a	n/a
42	CUX1	chr15:40885633-40886487	K562	blood:	n/a	n/a
43	ZKSCAN1	chr15:40885643-40887072	Hela-S3	cervix:	n/a	n/a
44	CEBPB	chr15:40885687-40886393	HepG2	liver:	n/a	n/a
45	NFIC	chr15:40885797-40886591	GM12878	blood:	n/a	chr15:40886323-40886340
46	TBP	chr15:40885414-40887116	GM12878	blood:	n/a	n/a
47	JUND	chr15:40885909-40886434	HepG2	liver:	n/a	chr15:40886313-40886322
48	SIN3AK20	chr15:40886308-40887000	HepG2	liver:	n/a	n/a
49	EP300	chr15:40885979-40886515	HepG2	liver:	n/a	n/a
50	MXI1	chr15:40885667-40887387	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40886149..40886965-chr15:41186125..41186636,2	K562	blood:
2	chr15:40856304..40858832-chr15:40886132..40888060,2	K562	blood:
3	chr15:40885583..40887494-chr15:40985320..40988301,2	K562	blood:
4	chr1:8938942..8939671-chr15:40886186..40886777,2	Hela-S3	cervix:
5	chr15:40884808..40888126-chr15:40896275..40900248,4	K562	blood:
6	chr15:40854296..40857804-chr15:40884735..40887632,3	K562	blood:
7	chr15:40886023..40886562-chr4:100871091..100871607,2	Hela-S3	cervix:
8	chr15:40861014..40861649-chr15:40886152..40886686,2	Hela-S3	cervix:
9	chr15:40884637..40889853-chr15:40895293..40899936,6	K562	blood:

Variant related genes	Relation type
CASC5	TF binding region
ENSG00000074800	Chromatin interaction
ENSG00000166133	Chromatin interaction
ENSG00000245322	Chromatin interaction
ENSG00000164032	Chromatin interaction
ENSG00000238559	Chromatin interaction
ENSG00000104142	Chromatin interaction
ENSG00000245849	Chromatin interaction
ENSG00000051180	Chromatin interaction
ENSG00000128891	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1037445	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10400890	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10400901	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10444817	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11070277	0.81[EUR][1000 genomes]
rs11070282	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11070285	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11070286	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11632061	0.91[EUR][1000 genomes]
rs11632370	0.91[EUR][1000 genomes]
rs11638742	0.81[EUR][1000 genomes]
rs11852670	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11852694	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11852828	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11854986	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11855334	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11855923	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11856802	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11858113	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11858938	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12591207	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12594548	0.81[EUR][1000 genomes]
rs12595610	0.81[EUR][1000 genomes]
rs12902568	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12904801	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12905162	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12912635	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12913697	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12914743	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16970851	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1811513	0.83[EUR][1000 genomes]
rs1813898	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1967368	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2412531	0.91[EUR][1000 genomes]
rs2412532	0.91[EUR][1000 genomes]
rs2412534	0.83[EUR][1000 genomes]
rs2412544	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2898996	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2924387	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2924388	0.82[EUR][1000 genomes]
rs2959536	0.81[EUR][1000 genomes]
rs3092979	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34845954	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35047458	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3751653	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4080706	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4410047	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4923875	0.81[EUR][1000 genomes]
rs4923876	0.91[EUR][1000 genomes]
rs4924478	0.81[EUR][1000 genomes]
rs4924479	0.81[EUR][1000 genomes]
rs4924480	0.81[EUR][1000 genomes]
rs4924481	0.91[EUR][1000 genomes]
rs62019916	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62019918	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6492951	0.81[EUR][1000 genomes]
rs6582	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71471881	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7169621	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7181074	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7182530	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7183790	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8026605	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8029384	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8034043	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8034048	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8036737	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8038407	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8041534	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs896795	0.91[EUR][1000 genomes]
rs976401	0.83[EUR][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	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs3751652	C15orf57	cis	Esophagus Mucosa	GTEx
rs3751652	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs3751652	RP11-111A22.1	cis	Nerve Tibial	GTEx
rs3751652	C15orf57	cis	Artery Aorta	GTEx
rs3751652	C15orf57	cis	Stomach	GTEx
rs3751652	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs3751652	RP11-111A22.1	cis	Artery Aorta	GTEx
rs3751652	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs3751652	ZFYVE19	cis	multi-tissue	Pritchard
rs3751652	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs3751652	C15orf57	cis	Heart Left Ventricle	GTEx
rs3751652	C15orf57	cis	Muscle Skeletal	GTEx
rs3751652	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs3751652	RP11-111A22.1	cis	Artery Tibial	GTEx
rs3751652	RP11-111A22.1	cis	lung	GTEx
rs3751652	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs3751652	C15orf57	cis	Esophagus Muscularis	GTEx
rs3751652	C15orf57	cis	Adipose Subcutaneous	GTEx
rs3751652	RP11-111A22.1	cis	Stomach	GTEx
rs3751652	C15orf57	cis	Artery Tibial	GTEx
rs3751652	C15orf57	cis	Thyroid	GTEx
rs3751652	C15orf57	cis	lung	GTEx
rs3751652	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs3751652	C15orf57	cis	Nerve Tibial	GTEx
rs3751652	CCDC32	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40885600-40887200	Active TSS	Fetal Brain Male	brain
2	chr15:40885600-40887400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:40885600-40887400	Active TSS	Fetal Kidney	kidney
4	chr15:40885600-40888200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr15:40885600-40888200	Active TSS	NHDF-Ad	bronchial
6	chr15:40885600-40888400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:40885800-40886600	Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr15:40885800-40886800	Active TSS	Primary B cells from cord blood	blood
9	chr15:40885800-40886800	Active TSS	Primary B cells from peripheral blood	blood
10	chr15:40885800-40886800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr15:40885800-40886800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
12	chr15:40885800-40886800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:40885800-40887200	Active TSS	Monocytes-CD14+_RO01746	blood
14	chr15:40885800-40887400	Active TSS	Fetal Thymus	thymus
15	chr15:40885800-40887800	Active TSS	K562	blood
16	chr15:40885800-40888000	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr15:40885800-40888000	Active TSS	Thymus	Thymus
18	chr15:40885800-40888400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:40886000-40886400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:40886000-40886400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:40886000-40886400	Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr15:40886000-40886400	Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr15:40886000-40886600	Active TSS	Primary hematopoietic stem cells	blood
24	chr15:40886000-40886600	Active TSS	Brain Anterior Caudate	brain
25	chr15:40886000-40886600	Active TSS	Brain Cingulate Gyrus	brain
26	chr15:40886000-40886600	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr15:40886000-40886600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr15:40886000-40886600	Active TSS	Pancreas	Pancrea
29	chr15:40886000-40886600	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr15:40886000-40886600	Active TSS	Rectal Smooth Muscle	rectum
31	chr15:40886000-40886600	Active TSS	Stomach Smooth Muscle	stomach
32	chr15:40886000-40886800	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr15:40886000-40886800	Active TSS	Primary monocytes fromperipheralblood	blood
34	chr15:40886000-40886800	Active TSS	Primary T cells from cord blood	blood
35	chr15:40886000-40886800	Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr15:40886000-40886800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:40886000-40886800	Active TSS	Brain Hippocampus Middle	brain
38	chr15:40886000-40887000	Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr15:40886000-40887000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr15:40886000-40887000	Active TSS	Brain Substantia Nigra	brain
41	chr15:40886000-40887200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr15:40886000-40887200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr15:40886000-40887200	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr15:40886000-40887200	Active TSS	Brain Angular Gyrus	brain
45	chr15:40886000-40887200	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr15:40886000-40887200	Active TSS	Esophagus	oesophagus
47	chr15:40886000-40887200	Active TSS	Fetal Intestine Small	intestine
48	chr15:40886000-40887200	Active TSS	Fetal Lung	lung
49	chr15:40886000-40887200	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr15:40886000-40887400	Active TSS	HUES48 Cell Line	embryonic stem cell

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