Variant report

Variant	rs28372775
Chromosome Location	chr4:88343704-88343705
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:534)
CpG islands
(count:122)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:534 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr4:88343556-88344042	K562	blood:	n/a	chr4:88343815-88343826
2	TAF1	chr4:88343537-88344103	PFSK-1	brain:	n/a	n/a
3	CHD2	chr4:88343556-88344357	Hela-S3	cervix:	n/a	n/a
4	TAF7	chr4:88343380-88344281	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr4:88343136-88344193	GM12891	blood:	n/a	n/a
6	HEY1	chr4:88343296-88344271	HepG2	liver:	n/a	n/a
7	POLR2A	chr4:88343432-88343989	HepG2	liver:	n/a	n/a
8	USF2	chr4:88343616-88344032	HepG2	liver:	n/a	n/a
9	EP300	chr4:88343512-88344192	GM12878	blood:	n/a	chr4:88343593-88343607
10	MAX	chr4:88343270-88344313	ECC-1	luminal epithelium:	n/a	n/a
11	NFIC	chr4:88343414-88344040	HepG2	liver:	n/a	n/a
12	CREB1	chr4:88343394-88344201	K562	blood:	n/a	n/a
13	ZNF143	chr4:88343389-88344188	GM12878	blood:	n/a	n/a
14	BHLHE40	chr4:88343407-88344493	GM12878	blood:	n/a	n/a
15	SPI1	chr4:88343500-88343767	K562	blood:	n/a	n/a
16	EP300	chr4:88343534-88344037	H1-hESC	embryonic stem cell:	n/a	chr4:88343593-88343607
17	JUND	chr4:88343383-88344353	K562	blood:	n/a	n/a
18	POLR2A	chr4:88343530-88344187	A549	lung:	n/a	n/a
19	YY1	chr4:88343526-88344216	GM12891	blood:	n/a	chr4:88343649-88343663
20	HCFC1	chr4:88342970-88344360	Hela-S3	cervix:	n/a	n/a
21	RELA	chr4:88343254-88344364	GM18951	blood:	n/a	n/a
22	NFYB	chr4:88343689-88344095	GM12878	blood:	n/a	n/a
23	CEBPD	chr4:88343531-88343873	HepG2	liver:	n/a	n/a
24	GABPA	chr4:88343609-88343892	A549	lung:	n/a	chr4:88343646-88343660
25	POLR2A	chr4:88343285-88344281	HepG2	liver:	n/a	n/a
26	RELA	chr4:88343273-88344230	GM19099	blood:	n/a	n/a
27	USF1	chr4:88343585-88344046	A549	lung:	n/a	chr4:88343815-88343826
28	TAF1	chr4:88343442-88344146	Hela-S3	cervix:	n/a	n/a
29	USF1	chr4:88343569-88344061	A549	lung:	n/a	chr4:88343815-88343826
30	SIN3AK20	chr4:88343313-88344252	MCF-7	breast:	n/a	n/a
31	ELF1	chr4:88343475-88343834	A549	lung:	n/a	n/a
32	RFX5	chr4:88343688-88343988	K562	blood:	n/a	n/a
33	RCOR1	chr4:88343386-88344100	GM12878	blood:	n/a	n/a
34	MYC	chr4:88343385-88344266	K562	blood:	n/a	n/a
35	NFIC	chr4:88343305-88344141	ECC-1	luminal epithelium:	n/a	n/a
36	SIN3AK20	chr4:88343469-88344120	PANC-1	pancreas:	n/a	n/a
37	POLR2A	chr4:88343068-88343948	K562	blood:	n/a	n/a
38	POLR2A	chr4:88343362-88344172	A549	lung:	n/a	n/a
39	USF2	chr4:88343609-88344013	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr4:88343355-88344215	HepG2	liver:	n/a	n/a
41	ATF3	chr4:88343562-88343871	GM12878	blood:	n/a	chr4:88343726-88343735
42	POLR2A	chr4:88343402-88344227	H1-hESC	embryonic stem cell:	n/a	n/a
43	ATF2	chr4:88343477-88344011	H1-hESC	embryonic stem cell:	n/a	n/a
44	TAF1	chr4:88343212-88344217	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr4:88343230-88344271	ECC-1	luminal epithelium:	n/a	n/a
46	GATA3	chr4:88343394-88344271	SK-N-SH	brain:	n/a	chr4:88343602-88343612
47	GATA3	chr4:88343529-88344163	A549	lung:	n/a	chr4:88343602-88343612
48	TCF12	chr4:88343458-88344030	A549	lung:	n/a	n/a
49	EP300	chr4:88343453-88344273	K562	blood:	n/a	chr4:88343593-88343607
50	RCOR1	chr4:88343422-88344214	K562	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:88343678-88343728	HCT-116	colon:	n/a
2	chr4:88343678-88343728	GM19239	blood:	n/a
3	chr4:88343678-88343728	SK-N-MC	brain:	n/a
4	chr4:88343678-88343728	HPAEpiC	pulmonary alveolar:	n/a
5	chr4:88343654-88343704	GM12878	blood:	n/a
6	chr4:88343678-88343728	AoSMC	blood vessel:	n/a
7	chr4:88343678-88343728	H1-hESC	embryonic stem cell:	embryo
8	chr4:88343678-88343728	HMEC	breast:	n/a
9	chr4:88343678-88343728	T-47D	breast:	n/a
10	chr4:88343654-88343704	NHBE	bronchial:	n/a
11	chr4:88343654-88343704	ECC-1	luminal epithelium:	n/a
12	chr4:88343678-88343728	BE2_C	brain:	n/a
13	chr4:88343678-88343728	HRCEpiC	kidney:	n/a
14	chr4:88343654-88343704	HPAEpiC	pulmonary alveolar:	n/a
15	chr4:88343654-88343704	HCF	heart:	n/a
16	chr4:88343654-88343704	Hepatocyte	liver:	n/a
17	chr4:88343654-88343704	SK-N-SH	brain:	n/a
18	chr4:88343654-88343704	HCT-116	colon:	n/a
19	chr4:88343678-88343728	NB4	blood:	n/a
20	chr4:88343654-88343704	HNPCEpiC	eye:	n/a
21	chr4:88343654-88343704	HRE	kidney:	n/a
22	chr4:88343654-88343704	HMEC	breast:	n/a
23	chr4:88343678-88343728	AG09319	gingival:	n/a
24	chr4:88343654-88343704	HAEpiC	amniotic membrane:	n/a
25	chr4:88343678-88343728	HL-60	blood:	n/a
26	chr4:88343654-88343704	BE2_C	brain:	n/a
27	chr4:88343654-88343704	HCM	heart:	n/a
28	chr4:88343678-88343728	PANC-1	pancreas:	n/a
29	chr4:88343654-88343704	NB4	blood:	n/a
30	chr4:88343678-88343728	SK-N-SH	brain:	n/a
31	chr4:88343678-88343728	PrEC	prostate:	n/a
32	chr4:88343654-88343704	LNCaP	prostate:	n/a
33	chr4:88343678-88343728	RPTEC	kidney:	n/a
34	chr4:88343678-88343728	HRPEpiC	eye:	n/a
35	chr4:88343654-88343704	NH-A	brain:	n/a
36	chr4:88343678-88343728	NHDF-neo	bronchial:	n/a
37	chr4:88343678-88343728	AG09309	skin:	n/a
38	chr4:88343654-88343704	AG04449	skin:	fetal
39	chr4:88343654-88343704	T-47D	breast:	n/a
40	chr4:88343678-88343728	NH-A	brain:	n/a
41	chr4:88343654-88343704	HIPEpiC	eye:	n/a
42	chr4:88343678-88343728	SK-N-SH_RA	brain:	n/a
43	chr4:88343654-88343704	SKMC	muscle:	n/a
44	chr4:88343678-88343728	HEEpiC	esophagus:	n/a
45	chr4:88343654-88343704	BJ	skin:	n/a
46	chr4:88343654-88343704	PrEC	prostate:	n/a
47	chr4:88343654-88343704	NT2-D1	testis:	n/a
48	chr4:88343654-88343704	GM06990	blood:	n/a
49	chr4:88343654-88343704	AoSMC	blood vessel:	n/a
50	chr4:88343678-88343728	SAEC	small airway:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr4:88310667..88314164-chr4:88342247..88345345,4	K562	blood:
2	chr4:88333084..88334930-chr4:88342115..88343742,2	MCF-7	breast:
3	chr4:88339085..88341655-chr4:88342092..88343723,2	MCF-7	breast:
4	chr4:88309813..88313902-chr4:88342245..88346379,5	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSD17B11-2	chr4:88341428-88343734	NONHSAT097311

No data

Variant related genes	Relation type
NUDT9	TF binding region
NUDT9	CpG island
ENSG00000251716	Chromatin interaction
ENSG00000198189	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10010988	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10025902	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10027786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10032597	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10035024	0.81[AMR][1000 genomes]
rs11945232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13103927	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13104303	0.81[MEX][hapmap]
rs13113575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13138404	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13138636	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13150578	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28406846	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28502849	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28609242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28630962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28701008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28736552	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34549877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35322242	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35371368	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35607673	0.81[AMR][1000 genomes]
rs4314250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4324526	0.81[MEX][hapmap]
rs6816224	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6854710	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7659182	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28372775	HSD17B13	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88342400-88344800	Active TSS	Brain Anterior Caudate	brain
2	chr4:88342400-88345400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:88342400-88345400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr4:88342600-88345000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr4:88342600-88345400	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr4:88342600-88345400	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr4:88342600-88346000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr4:88342800-88344800	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr4:88342800-88344800	Active TSS	Brain Hippocampus Middle	brain
10	chr4:88342800-88345000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:88342800-88345000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:88342800-88345000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:88342800-88345000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:88343000-88343800	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr4:88343000-88344400	Active TSS	Esophagus	oesophagus
16	chr4:88343000-88344600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr4:88343000-88344600	Active TSS	Osteobl	bone
18	chr4:88343000-88344800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:88343000-88344800	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr4:88343000-88344800	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr4:88343000-88344800	Active TSS	Rectal Smooth Muscle	rectum
22	chr4:88343000-88344800	Active TSS	A549	lung
23	chr4:88343000-88344800	Active TSS	HMEC	breast
24	chr4:88343000-88344800	Active TSS	NHEK	skin
25	chr4:88343000-88345000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr4:88343000-88345000	Active TSS	Colonic Mucosa	Colon
27	chr4:88343000-88345000	Active TSS	HSMMtube	muscle
28	chr4:88343000-88345000	Active TSS	NHDF-Ad	bronchial
29	chr4:88343000-88345200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:88343000-88345200	Active TSS	NHLF	lung
31	chr4:88343000-88345400	Active TSS	H9 Cell Line	embryonic stem cell
32	chr4:88343000-88345400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:88343000-88345400	Active TSS	Ovary	ovary
34	chr4:88343000-88345800	Active TSS	HSMM	muscle
35	chr4:88343200-88344200	Active TSS	Primary T cells from cord blood	blood
36	chr4:88343200-88344400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:88343200-88344400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:88343200-88344400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr4:88343200-88344400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr4:88343200-88344400	Active TSS	Gastric	stomach
41	chr4:88343200-88344400	Active TSS	Lung	lung
42	chr4:88343200-88344600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr4:88343200-88344600	Active TSS	Placenta Amnion	Placenta Amnion
44	chr4:88343200-88344600	Active TSS	Dnd41	blood
45	chr4:88343200-88344800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr4:88343200-88344800	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr4:88343200-88344800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:88343200-88344800	Active TSS	Brain Angular Gyrus	brain
49	chr4:88343200-88344800	Active TSS	Fetal Heart	heart
50	chr4:88343200-88344800	Active TSS	Skeletal Muscle Male	skeletal muscle

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