Variant report

Variant	rs3753793
Chromosome Location	chr1:86045888-86045889
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:102)
CpG islands
(count:61)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:102 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr1:86045705-86047615	Hela-S3	cervix:	n/a	n/a
2	TCF7L2	chr1:86045710-86047578	Hela-S3	cervix:	n/a	chr1:86047350-86047360 chr1:86045792-86045801
3	POLR2A	chr1:86045313-86051202	ProgFib	skin:	n/a	n/a
4	POLR2A	chr1:86041793-86051199	HUVEC	blood vessel:	n/a	n/a
5	SMC3	chr1:86045729-86047898	Hela-S3	cervix:	n/a	n/a
6	MAFK	chr1:86045881-86045894	K562	blood:	n/a	n/a
7	TAF1	chr1:86045685-86048404	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:86045762-86045955	H1-hESC	embryonic stem cell:	n/a	n/a
9	TBP	chr1:86045223-86048449	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:86045842-86049091	Hela-S3	cervix:	n/a	n/a
11	NFIC	chr1:86045561-86049147	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr1:86041833-86052222	HUVEC	blood vessel:	n/a	n/a
13	CHD2	chr1:86045850-86047554	Hela-S3	cervix:	n/a	chr1:86046866-86046876 chr1:86046027-86046037
14	MYC	chr1:86045886-86047264	K562	blood:	n/a	chr1:86046475-86046485
15	POLR2A	chr1:86041771-86051250	HUVEC	blood vessel:	n/a	n/a
16	GATA3	chr1:86045616-86047524	A549	lung:	n/a	chr1:86046062-86046071
17	CHD1	chr1:86041753-86052318	IMR90	lung:	n/a	chr1:86046866-86046876 chr1:86046027-86046037 chr1:86044526-86044536
18	SMARCC1	chr1:86045796-86047730	Hela-S3	cervix:	n/a	n/a
19	STAT3	chr1:86045732-86046388	MCF10A-Er-Src	breast:	n/a	chr1:86045971-86045979
20	STAT3	chr1:86045764-86045955	MCF10A-Er-Src	breast:	n/a	n/a
21	MXI1	chr1:86045681-86047893	Hela-S3	cervix:	n/a	n/a
22	FOS	chr1:86045685-86046405	MCF10A-Er-Src	breast:	n/a	chr1:86045813-86045824
23	MAX	chr1:86045774-86049318	Hela-S3	cervix:	n/a	chr1:86046475-86046485
24	MYC	chr1:86045696-86045963	MCF10A-Er-Src	breast:	n/a	n/a
25	ZBTB7A	chr1:86045722-86047551	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr1:86041854-86051160	PANC-1	pancreas:	n/a	n/a
27	MAX	chr1:86045865-86047536	ECC-1	luminal epithelium:	n/a	chr1:86046475-86046485
28	MAZ	chr1:86045865-86047312	K562	blood:	n/a	chr1:86046475-86046485
29	SIN3A	chr1:86045288-86048435	H1-hESC	embryonic stem cell:	n/a	chr1:86046470-86046479 chr1:86046767-86046778
30	REST	chr1:86045888-86046709	A549	lung:	n/a	chr1:86046314-86046324
31	MXI1	chr1:86045876-86047653	HepG2	liver:	n/a	n/a
32	POLR2A	chr1:86041016-86051875	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr1:86045681-86049269	H1-hESC	embryonic stem cell:	n/a	n/a
34	TBP	chr1:86045833-86047425	K562	blood:	n/a	n/a
35	SIN3AK20	chr1:86045675-86046026	PFSK-1	brain:	n/a	n/a
36	MAX	chr1:86045644-86047667	A549	lung:	n/a	chr1:86046475-86046485 chr1:86045681-86045691
37	MAFK	chr1:86045829-86045916	HepG2	liver:	n/a	n/a
38	POLR2A	chr1:86045361-86051797	MCF10A-Er-Src	breast:	n/a	n/a
39	CREB1	chr1:86045722-86047311	HepG2	liver:	n/a	n/a
40	POLR2A	chr1:86045835-86047380	K562	blood:	n/a	n/a
41	SP1	chr1:86045816-86046665	A549	lung:	n/a	n/a
42	TCF12	chr1:86045702-86048611	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr1:86044532-86052365	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr1:86045758-86050899	Hela-S3	cervix:	n/a	n/a
45	CHD1	chr1:86044932-86050997	H1-hESC	embryonic stem cell:	n/a	chr1:86046866-86046876 chr1:86046027-86046037
46	ZNF143	chr1:86045786-86046314	K562	blood:	n/a	n/a
47	FOS	chr1:86045755-86045947	MCF10A-Er-Src	breast:	n/a	chr1:86045813-86045824
48	GTF2F1	chr1:86045793-86045924	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr1:86045764-86049296	Hela-S3	cervix:	n/a	n/a
50	FOXA1	chr1:86045707-86046054	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:86045841-86045891	HPAEpiC	pulmonary alveolar:	n/a
2	chr1:86045841-86045891	AG09319	gingival:	n/a
3	chr1:86045841-86045891	K562	blood:	n/a
4	chr1:86045841-86045891	GM12891	blood:	n/a
5	chr1:86045841-86045891	CMK	blood:	n/a
6	chr1:86045841-86045891	RPTEC	kidney:	n/a
7	chr1:86045841-86045891	AG10803	skin:	n/a
8	chr1:86045841-86045891	Caco-2	colon:	n/a
9	chr1:86045841-86045891	HCM	heart:	n/a
10	chr1:86045841-86045891	AG04449	skin:	fetal
11	chr1:86045841-86045891	ovcar-3	ovarian:	n/a
12	chr1:86045841-86045891	HRPEpiC	eye:	n/a
13	chr1:86045841-86045891	LNCaP	prostate:	n/a
14	chr1:86045841-86045891	NB4	blood:	n/a
15	chr1:86045841-86045891	ProgFib	skin:	n/a
16	chr1:86045841-86045891	NH-A	brain:	n/a
17	chr1:86045841-86045891	GM12878	blood:	n/a
18	chr1:86045841-86045891	SK-N-MC	brain:	n/a
19	chr1:86045841-86045891	GM19239	blood:	n/a
20	chr1:86045841-86045891	NHDF-neo	bronchial:	n/a
21	chr1:86045841-86045891	A549	lung:	n/a
22	chr1:86045841-86045891	HNPCEpiC	eye:	n/a
23	chr1:86045841-86045891	AG09309	skin:	n/a
24	chr1:86045841-86045891	Hela-S3	cervix:	n/a
25	chr1:86045841-86045891	HEEpiC	esophagus:	n/a
26	chr1:86045841-86045891	SAEC	small airway:	n/a
27	chr1:86045841-86045891	IMR90	lung:	fetal
28	chr1:86045841-86045891	NT2-D1	testis:	n/a
29	chr1:86045841-86045891	SK-N-SH_RA	brain:	n/a
30	chr1:86045841-86045891	AG04450	lung:	fetal
31	chr1:86045841-86045891	MCF-7	breast:	n/a
32	chr1:86045841-86045891	PANC-1	pancreas:	n/a
33	chr1:86045841-86045891	HCF	heart:	n/a
34	chr1:86045841-86045891	MCF10A-Er-Src	breast:	n/a
35	chr1:86045841-86045891	U87	brain:	n/a
36	chr1:86045841-86045891	HepG2	liver:	n/a
37	chr1:86045841-86045891	BE2_C	brain:	n/a
38	chr1:86045841-86045891	ECC-1	luminal epithelium:	n/a
39	chr1:86045841-86045891	SK-N-SH	brain:	n/a
40	chr1:86045841-86045891	HAEpiC	amniotic membrane:	n/a
41	chr1:86045841-86045891	AoSMC	blood vessel:	n/a
42	chr1:86045841-86045891	SKMC	muscle:	n/a
43	chr1:86045841-86045891	HCT-116	colon:	n/a
44	chr1:86045841-86045891	H1-hESC	embryonic stem cell:	embryo
45	chr1:86045841-86045891	BJ	skin:	n/a
46	chr1:86045841-86045891	HRCEpiC	kidney:	n/a
47	chr1:86045841-86045891	Jurkat	blood:	n/a
48	chr1:86045841-86045891	GM06990	blood:	n/a
49	chr1:86045841-86045891	PFSK-1	brain:	n/a
50	chr1:86045841-86045891	HUVEC	blood vessel:	n/a

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:86044508..86046201-chr1:86070309..86072884,2	K562	blood:
2	chr1:86045233..86051336-chr1:86057804..86069814,19	K562	blood:
3	chr1:86043660..86051626-chr1:86167839..86177430,17	K562	blood:
4	chr1:85930091..85932037-chr1:86045511..86048058,4	MCF-7	breast:
5	chr1:85929622..85931400-chr1:86044914..86046491,2	MCF-7	breast:
6	chr1:86045884..86046584-chr7:21984850..21985841,2	Hela-S3	cervix:
7	chr1:86045777..86046557-chr3:171757245..171757867,2	Hela-S3	cervix:
8	chr1:85958709..85962572-chr1:86044730..86049172,10	MCF-7	breast:
9	chr1:85959814..85963220-chr1:86043447..86048399,5	MCF-7	breast:
10	chr1:85739753..85743262-chr1:86045535..86049012,3	K562	blood:
11	chr1:86043937..86050216-chr1:86058297..86066765,12	K562	blood:
12	chr1:85739584..85746681-chr1:86042287..86049012,10	K562	blood:

No data

Variant related genes	Relation type
CYR61	TF binding region
DDAH1	TF binding region
ENSG00000272691	TF binding region
CYR61	CpG island
DDAH1	CpG island
ENSG00000272691	CpG island
ENSG00000230285	Chromatin interaction
ENSG00000164649	Chromatin interaction
ENSG00000117174	Chromatin interaction
ENSG00000075420	Chromatin interaction
ENSG00000199934	Chromatin interaction
ENSG00000142867	Chromatin interaction
ENSG00000153904	Chromatin interaction
ENSG00000223653	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10873708	0.82[CEU][hapmap]
rs3753794	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3753795	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs721471	0.84[CHD][hapmap];0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3753793	CLCA2	cis	cerebellum	SCAN
rs3753793	DNASE2B	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86041800-86047800	Active TSS	Aorta	Aorta
2	chr1:86043000-86046600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:86044600-86046200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:86044600-86046200	Flanking Active TSS	Osteobl	bone
5	chr1:86045000-86047200	Active TSS	H9 Cell Line	embryonic stem cell
6	chr1:86045200-86046200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:86045200-86046200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
8	chr1:86045200-86046200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr1:86045200-86046200	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr1:86045200-86046600	Bivalent/Poised TSS	Fetal Brain Female	brain
11	chr1:86045200-86047000	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:86045200-86047400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:86045200-86047600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:86045200-86047600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:86045200-86048600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr1:86045400-86046000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
17	chr1:86045400-86046000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr1:86045400-86046000	Flanking Active TSS	Fetal Stomach	stomach
19	chr1:86045400-86046400	Flanking Active TSS	Fetal Muscle Leg	muscle
20	chr1:86045400-86046600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:86045400-86046600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
22	chr1:86045400-86046600	Active TSS	Esophagus	oesophagus
23	chr1:86045400-86046600	Active TSS	NHLF	lung
24	chr1:86045400-86046800	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr1:86045400-86047200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:86045400-86047200	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr1:86045400-86047200	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr1:86045400-86047200	Active TSS	A549	lung
29	chr1:86045400-86047200	Active TSS	HSMMtube	muscle
30	chr1:86045400-86047200	Active TSS	NH-A	brain
31	chr1:86045400-86047200	Active TSS	NHDF-Ad	bronchial
32	chr1:86045400-86047600	Active TSS	Colon Smooth Muscle	Colon
33	chr1:86045400-86047800	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr1:86045400-86047800	Active TSS	Ovary	ovary
35	chr1:86045400-86048000	Active TSS	Rectal Smooth Muscle	rectum
36	chr1:86045400-86048600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:86045400-86048800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:86045600-86046200	Flanking Active TSS	Fetal Muscle Trunk	muscle
39	chr1:86045600-86046600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:86045600-86046600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:86045600-86046600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:86045600-86046600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:86045600-86046600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:86045600-86046600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:86045600-86046600	Active TSS	HUVEC	blood vessel
46	chr1:86045600-86046800	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr1:86045600-86047000	Active TSS	HMEC	breast
48	chr1:86045600-86047200	Active TSS	H1 Cell Line	embryonic stem cell
49	chr1:86045600-86047200	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr1:86045600-86047400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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