Variant report

Variant	rs2453596
Chromosome Location	chr17:19483571-19483572
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr17:19483447-19483571	H1-hESC	embryonic stem cell:	n/a	n/a
2	FOSL2	chr17:19483396-19483833	HepG2	liver:	n/a	n/a
3	MAX	chr17:19482659-19483719	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr17:19483494-19483695	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:19483554-19483604	SK-N-MC	brain:	n/a
2	chr17:19483554-19483604	HL-60	blood:	n/a
3	chr17:19483554-19483604	HRE	kidney:	n/a
4	chr17:19483554-19483604	A549	lung:	n/a
5	chr17:19483554-19483604	H1-hESC	embryonic stem cell:	embryo
6	chr17:19483554-19483604	GM12878	blood:	n/a
7	chr17:19483554-19483604	PrEC	prostate:	n/a
8	chr17:19483554-19483604	ECC-1	luminal epithelium:	n/a
9	chr17:19483554-19483604	LNCaP	prostate:	n/a
10	chr17:19483554-19483604	SAEC	small airway:	n/a
11	chr17:19483554-19483604	Hela-S3	cervix:	n/a
12	chr17:19483554-19483604	BE2_C	brain:	n/a
13	chr17:19483554-19483604	BJ	skin:	n/a
14	chr17:19483554-19483604	HPAEpiC	pulmonary alveolar:	n/a
15	chr17:19483554-19483604	GM19239	blood:	n/a
16	chr17:19483554-19483604	MCF-7	breast:	n/a
17	chr17:19483554-19483604	PFSK-1	brain:	n/a
18	chr17:19483554-19483604	HCM	heart:	n/a
19	chr17:19483554-19483604	NT2-D1	testis:	n/a
20	chr17:19483554-19483604	HRCEpiC	kidney:	n/a
21	chr17:19483554-19483604	U87	brain:	n/a
22	chr17:19483554-19483604	ovcar-3	ovarian:	n/a
23	chr17:19483554-19483604	HRPEpiC	eye:	n/a
24	chr17:19483554-19483604	NHDF-neo	bronchial:	n/a
25	chr17:19483554-19483604	MCF10A-Er-Src	breast:	n/a
26	chr17:19483554-19483604	PANC-1	pancreas:	n/a
27	chr17:19483554-19483604	GM06990	blood:	n/a
28	chr17:19483554-19483604	K562	blood:	n/a
29	chr17:19483554-19483604	HCPEpiC	choroid plexus:	n/a
30	chr17:19483554-19483604	AG09309	skin:	n/a
31	chr17:19483554-19483604	GM12892	blood:	n/a
32	chr17:19483554-19483604	SK-N-SH_RA	brain:	n/a
33	chr17:19483554-19483604	HIPEpiC	eye:	n/a
34	chr17:19483554-19483604	Hepatocyte	liver:	n/a
35	chr17:19483554-19483604	HMEC	breast:	n/a
36	chr17:19483554-19483604	ProgFib	skin:	n/a
37	chr17:19483554-19483604	AG09319	gingival:	n/a
38	chr17:19483554-19483604	NH-A	brain:	n/a
39	chr17:19483554-19483604	Caco-2	colon:	n/a
40	chr17:19483554-19483604	HAEpiC	amniotic membrane:	n/a
41	chr17:19483554-19483604	AG04449	skin:	fetal
42	chr17:19483554-19483604	GM12891	blood:	n/a
43	chr17:19483554-19483604	IMR90	lung:	fetal
44	chr17:19483554-19483604	SK-N-SH	brain:	n/a
45	chr17:19483554-19483604	SKMC	muscle:	n/a
46	chr17:19483554-19483604	NB4	blood:	n/a
47	chr17:19483554-19483604	Jurkat	blood:	n/a
48	chr17:19483554-19483604	T-47D	breast:	n/a
49	chr17:19483554-19483604	HEEpiC	esophagus:	n/a
50	chr17:19483554-19483604	HNPCEpiC	eye:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC47A1-1	chr17:19483547-19483648	NONHSAT146500

No data

Variant related genes	Relation type
ENSG00000228983	TF binding region
ENSG00000228983	CpG island

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10735	0.94[EUR][1000 genomes]
rs2249885	0.91[EUR][1000 genomes]
rs2440167	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2453594	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2453595	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7212622	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428337	chr17:19340045-19585774	Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1061408	chr17:19458185-19613357	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2453596	CTD-2104P17.1	cis	Nerve Tibial	GTEx
rs2453596	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19464000-19483800	Weak transcription	A549	lung
2	chr17:19481200-19485600	Weak transcription	HepG2	liver
3	chr17:19482600-19483800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr17:19482600-19483800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr17:19482600-19484000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr17:19482600-19484000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr17:19482600-19484000	Bivalent Enhancer	Placenta	Placenta
8	chr17:19482800-19483600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:19482800-19483600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr17:19482800-19483600	Active TSS	Brain Anterior Caudate	brain
11	chr17:19482800-19483600	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
12	chr17:19482800-19483600	Active TSS	Rectal Smooth Muscle	rectum
13	chr17:19482800-19483800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr17:19482800-19483800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr17:19482800-19483800	Active TSS	H9 Cell Line	embryonic stem cell
16	chr17:19482800-19483800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
17	chr17:19482800-19483800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr17:19482800-19483800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
19	chr17:19482800-19483800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr17:19482800-19483800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
21	chr17:19482800-19484000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
22	chr17:19482800-19484000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
23	chr17:19482800-19484000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr17:19482800-19484000	Active TSS	Brain Germinal Matrix	brain
25	chr17:19483000-19483600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
26	chr17:19483000-19483600	Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr17:19483000-19483600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr17:19483000-19483600	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
29	chr17:19483000-19483600	Active TSS	Ovary	ovary
30	chr17:19483000-19483600	Bivalent/Poised TSS	Thymus	Thymus
31	chr17:19483000-19483800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr17:19483000-19483800	Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr17:19483000-19483800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr17:19483000-19483800	Active TSS	Aorta	Aorta
35	chr17:19483000-19483800	Bivalent/Poised TSS	Fetal Brain Female	brain
36	chr17:19483000-19483800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
37	chr17:19483000-19483800	Active TSS	Psoas Muscle	Psoas
38	chr17:19483000-19483800	Active TSS	Right Atrium	heart
39	chr17:19483000-19484000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr17:19483000-19484000	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr17:19483000-19484200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
42	chr17:19483200-19483600	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
43	chr17:19483200-19483600	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
44	chr17:19483200-19483600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
45	chr17:19483200-19483600	Active TSS	Esophagus	oesophagus
46	chr17:19483200-19483600	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr17:19483200-19483600	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
48	chr17:19483200-19483600	Active TSS	Left Ventricle	heart
49	chr17:19483200-19483600	Active TSS	HUVEC	blood vessel
50	chr17:19483200-19483600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood

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