Variant report

Variant	rs3742970
Chromosome Location	chr15:43622265-43622266
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:283)
CpG islands
(count:61)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:283 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:43622100-43623100	HUVEC	blood vessel:	n/a	n/a
2	HEY1	chr15:43622232-43623107	HepG2	liver:	n/a	n/a
3	EP300	chr15:43621959-43623217	ECC-1	luminal epithelium:	n/a	chr15:43622826-43622833
4	MYC	chr15:43621964-43622294	MCF-7	breast:	n/a	n/a
5	POLR2A	chr15:43622198-43623182	SK-N-MC	brain:	n/a	n/a
6	MAX	chr15:43621774-43623049	K562	blood:	n/a	n/a
7	POLR2A	chr15:43622193-43623157	HepG2	liver:	n/a	n/a
8	HEY1	chr15:43621897-43623192	K562	blood:	n/a	n/a
9	HEY1	chr15:43622146-43623190	HepG2	liver:	n/a	n/a
10	SREBP2	chr15:43621854-43623679	GM12878	blood:	n/a	n/a
11	POLR2A	chr15:43622095-43623110	K562	blood:	n/a	n/a
12	RAD21	chr15:43622085-43622781	ECC-1	luminal epithelium:	n/a	n/a
13	MAX	chr15:43621968-43623152	MCF-7	breast:	n/a	n/a
14	CREB1	chr15:43621724-43623112	H1-hESC	embryonic stem cell:	n/a	n/a
15	CREB1	chr15:43621793-43623204	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr15:43622148-43623153	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr15:43620770-43623194	K562	blood:	n/a	n/a
18	E2F4	chr15:43621990-43623064	Hela-S3	cervix:	n/a	chr15:43622437-43622448
19	POLR2A	chr15:43621900-43623162	HEK293	kidney:	n/a	n/a
20	POLR2A	chr15:43621953-43623314	PANC-1	pancreas:	n/a	n/a
21	MXI1	chr15:43622159-43623251	Hela-S3	cervix:	n/a	n/a
22	REST	chr15:43621406-43623418	H1-neurons	neurons:	n/a	chr15:43623129-43623143
23	RUNX3	chr15:43621857-43623193	GM12878	blood:	n/a	n/a
24	YY1	chr15:43622183-43623111	K562	blood:	n/a	n/a
25	CTCF	chr15:43622160-43622310	GM12875	blood:	n/a	n/a
26	POLR2A	chr15:43622077-43623199	GM12878	blood:	n/a	n/a
27	MYBL2	chr15:43622088-43623080	HepG2	liver:	n/a	n/a
28	FOXM1	chr15:43622215-43623158	GM12878	blood:	n/a	n/a
29	TBP	chr15:43621635-43623291	K562	blood:	n/a	n/a
30	E2F6	chr15:43622068-43623069	H1-hESC	embryonic stem cell:	n/a	n/a
31	HMGN3	chr15:43621837-43622798	K562	blood:	n/a	n/a
32	MAX	chr15:43621854-43623251	HepG2	liver:	n/a	n/a
33	PML	chr15:43621649-43623269	GM12878	blood:	n/a	n/a
34	NRF1	chr15:43621998-43623116	GM12878	blood:	n/a	chr15:43622502-43622513
35	MAX	chr15:43621880-43623238	ECC-1	luminal epithelium:	n/a	n/a
36	TCF12	chr15:43622023-43623213	A549	lung:	n/a	n/a
37	E2F6	chr15:43622045-43623018	A549	lung:	n/a	n/a
38	MYC	chr15:43621869-43623350	K562	blood:	n/a	n/a
39	MAX	chr15:43621693-43623301	A549	lung:	n/a	n/a
40	SIN3AK20	chr15:43621669-43623226	MCF-7	breast:	n/a	n/a
41	TEAD4	chr15:43622242-43623212	K562	blood:	n/a	n/a
42	POLR2A	chr15:43622161-43623067	GM12878	blood:	n/a	n/a
43	TAF1	chr15:43622264-43623168	Hela-S3	cervix:	n/a	n/a
44	MAX	chr15:43621914-43623175	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr15:43621709-43623279	GM12878	blood:	n/a	n/a
46	USF2	chr15:43622050-43623091	GM12878	blood:	n/a	n/a
47	SMARCB1	chr15:43621734-43623261	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr15:43622115-43623164	HUVEC	blood vessel:	n/a	n/a
49	USF2	chr15:43622068-43622676	H1-hESC	embryonic stem cell:	n/a	n/a
50	GABPA	chr15:43622175-43623277	A549	lung:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:43622253-43622303	SK-N-SH_RA	brain:	n/a
2	chr15:43622253-43622303	SK-N-MC	brain:	n/a
3	chr15:43622253-43622303	NH-A	brain:	n/a
4	chr15:43622253-43622303	PANC-1	pancreas:	n/a
5	chr15:43622253-43622303	NHBE	bronchial:	n/a
6	chr15:43622253-43622303	NHDF-neo	bronchial:	n/a
7	chr15:43622253-43622303	SKMC	muscle:	n/a
8	chr15:43622253-43622303	GM12891	blood:	n/a
9	chr15:43622253-43622303	NT2-D1	testis:	n/a
10	chr15:43622253-43622303	HMEC	breast:	n/a
11	chr15:43622253-43622303	HCM	heart:	n/a
12	chr15:43622253-43622303	HRPEpiC	eye:	n/a
13	chr15:43622253-43622303	SK-N-SH	brain:	n/a
14	chr15:43622253-43622303	AG09319	gingival:	n/a
15	chr15:43622253-43622303	HUVEC	blood vessel:	n/a
16	chr15:43622253-43622303	HRCEpiC	kidney:	n/a
17	chr15:43622253-43622303	GM12892	blood:	n/a
18	chr15:43622253-43622303	HCF	heart:	n/a
19	chr15:43622253-43622303	Hepatocyte	liver:	n/a
20	chr15:43622253-43622303	MCF10A-Er-Src	breast:	n/a
21	chr15:43622253-43622303	ECC-1	luminal epithelium:	n/a
22	chr15:43622253-43622303	AG04449	skin:	fetal
23	chr15:43622253-43622303	HepG2	liver:	n/a
24	chr15:43622253-43622303	HCT-116	colon:	n/a
25	chr15:43622253-43622303	HPAEpiC	pulmonary alveolar:	n/a
26	chr15:43622253-43622303	AoSMC	blood vessel:	n/a
27	chr15:43622253-43622303	HL-60	blood:	n/a
28	chr15:43622253-43622303	HRE	kidney:	n/a
29	chr15:43622253-43622303	IMR90	lung:	fetal
30	chr15:43622253-43622303	RPTEC	kidney:	n/a
31	chr15:43622253-43622303	GM06990	blood:	n/a
32	chr15:43622253-43622303	U87	brain:	n/a
33	chr15:43622253-43622303	BE2_C	brain:	n/a
34	chr15:43622253-43622303	PFSK-1	brain:	n/a
35	chr15:43622253-43622303	SAEC	small airway:	n/a
36	chr15:43622253-43622303	BJ	skin:	n/a
37	chr15:43622253-43622303	NB4	blood:	n/a
38	chr15:43622253-43622303	GM19239	blood:	n/a
39	chr15:43622253-43622303	ovcar-3	ovarian:	n/a
40	chr15:43622253-43622303	A549	lung:	n/a
41	chr15:43622253-43622303	AG10803	skin:	n/a
42	chr15:43622253-43622303	HIPEpiC	eye:	n/a
43	chr15:43622253-43622303	AG04450	lung:	fetal
44	chr15:43622253-43622303	CMK	blood:	n/a
45	chr15:43622253-43622303	HNPCEpiC	eye:	n/a
46	chr15:43622253-43622303	HEEpiC	esophagus:	n/a
47	chr15:43622253-43622303	T-47D	breast:	n/a
48	chr15:43622253-43622303	HEK293	kidney:	embryo
49	chr15:43622253-43622303	H1-hESC	embryonic stem cell:	embryo
50	chr15:43622253-43622303	Caco-2	colon:	n/a

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:43397435..43400079-chr15:43619938..43624138,3	K562	blood:
2	chr15:43621803..43624734-chr15:43667473..43669999,2	K562	blood:
3	chr15:43620224..43622600-chr15:43663902..43665478,2	MCF-7	breast:
4	chr15:43620805..43624764-chr15:43626235..43634573,14	K562	blood:
5	chr15:43476272..43478901-chr15:43620777..43622927,4	K562	blood:
6	chr15:43621078..43623590-chr15:43801793..43804270,2	MCF-7	breast:
7	chr15:43476610..43478211-chr15:43620895..43622509,2	K562	blood:
8	chr15:43618581..43624264-chr15:43661265..43664929,7	MCF-7	breast:
9	chr15:43622007..43622765-chr17:39845114..39845836,3	Hela-S3	cervix:
10	chr15:43621444..43623700-chr15:43661759..43663409,2	MCF-7	breast:
11	chr15:43619535..43624096-chr15:43662038..43665421,4	K562	blood:
12	chr15:43621834..43622636-chr5:81267421..81268117,2	Hela-S3	cervix:
13	chr15:43621044..43624825-chr15:43626235..43637209,16	K562	blood:
14	chr15:43500155..43503014-chr15:43621772..43625357,3	K562	blood:
15	chr15:43571338..43574214-chr15:43618657..43622685,4	K562	blood:
16	chr15:43620486..43624109-chr15:43661175..43665421,4	K562	blood:
17	chr1:22109386..22110022-chr15:43622257..43623111,2	Hela-S3	cervix:
18	chr15:43479061..43481710-chr15:43621878..43623729,2	K562	blood:
19	chr15:43512947..43514821-chr15:43621121..43624112,2	K562	blood:

No data

Variant related genes	Relation type
ADAL	TF binding region
ADAL	CpG island
ENSG00000173812	Chromatin interaction
ENSG00000166947	Chromatin interaction
ENSG00000168803	Chromatin interaction
ENSG00000090686	Chromatin interaction
ENSG00000152348	Chromatin interaction
ENSG00000159459	Chromatin interaction
ENSG00000261687	Chromatin interaction
ENSG00000067369	Chromatin interaction
ENSG00000137822	Chromatin interaction
ENSG00000140265	Chromatin interaction
ENSG00000166963	Chromatin interaction
ENSG00000166946	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs16957709	1.00[LWK][hapmap];0.81[MKK][hapmap];1.00[AFR][1000 genomes]
rs9652444	0.82[TSI][hapmap]

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	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1512	chr15:43616834-43661646	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs3742970	ADAL	cis	Adipose Subcutaneous	GTEx
rs3742970	ELL3	cis	lymphoblastoid	seeQTL
rs3742970	ADAL	cis	Artery Tibial	GTEx
rs3742970	ENSG00000168806	cis	multi-tissue	Pritchard
rs3742970	C15orf63	cis	lymphoblastoid	seeQTL
rs3742970	ADAL	cis	Artery Aorta	GTEx
rs3742970	SERF2	cis	lymphoblastoid	seeQTL
rs3742970	ADAL	cis	lung	GTEx
rs3742970	ADAL	cis	Skin Sun Exposed Lower leg	GTEx
rs3742970	ADAL	cis	Thyroid	GTEx
rs3742970	ADAL	cis	Esophagus Muscularis	GTEx
rs3742970	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs3742970	ADAL	cis	Stomach	GTEx
rs3742970	ADAL	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43620800-43624000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:43621000-43622400	Flanking Active TSS	HMEC	breast
3	chr15:43621200-43622400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
4	chr15:43621200-43623200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr15:43621200-43623400	Active TSS	Aorta	Aorta
6	chr15:43621200-43623800	Active TSS	Psoas Muscle	Psoas
7	chr15:43621400-43622400	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr15:43621400-43622400	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr15:43621400-43622400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:43621400-43622400	Flanking Active TSS	Colonic Mucosa	Colon
11	chr15:43621400-43622400	Flanking Active TSS	Placenta	Placenta
12	chr15:43621400-43622400	Flanking Active TSS	Fetal Thymus	thymus
13	chr15:43621400-43623400	Active TSS	A549	lung
14	chr15:43621400-43623400	Flanking Active TSS	HUVEC	blood vessel
15	chr15:43621400-43623800	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr15:43621600-43622400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr15:43621600-43622400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr15:43621600-43622800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr15:43621600-43623200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:43621600-43623200	Active TSS	Ovary	ovary
21	chr15:43621600-43623400	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr15:43621600-43623400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr15:43621600-43623400	Active TSS	Rectal Smooth Muscle	rectum
24	chr15:43621600-43623600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr15:43621600-43623600	Active TSS	H9 Cell Line	embryonic stem cell
26	chr15:43621600-43623800	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr15:43621800-43622400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr15:43621800-43623000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:43621800-43623000	Active TSS	Esophagus	oesophagus
30	chr15:43621800-43623000	Active TSS	Fetal Brain Male	brain
31	chr15:43621800-43623000	Active TSS	Fetal Brain Female	brain
32	chr15:43621800-43623200	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr15:43621800-43623200	Active TSS	Brain Cingulate Gyrus	brain
34	chr15:43621800-43623200	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr15:43621800-43623200	Active TSS	Fetal Intestine Large	intestine
36	chr15:43621800-43623200	Active TSS	Fetal Kidney	kidney
37	chr15:43621800-43623200	Active TSS	Fetal Lung	lung
38	chr15:43621800-43623200	Active TSS	Gastric	stomach
39	chr15:43621800-43623200	Active TSS	Lung	lung
40	chr15:43621800-43623200	Active TSS	Pancreas	Pancrea
41	chr15:43621800-43623200	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr15:43621800-43623200	Active TSS	Small Intestine	intestine
43	chr15:43621800-43623200	Active TSS	Stomach Mucosa	stomach
44	chr15:43621800-43623200	Active TSS	NHEK	skin
45	chr15:43621800-43623400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr15:43621800-43623400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:43621800-43623400	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr15:43621800-43623400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr15:43621800-43623400	Active TSS	K562	blood
50	chr15:43621800-43623400	Active TSS	NHLF	lung

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