Variant report

Variant	rs55824708
Chromosome Location	chr4:88343290-88343291
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:126)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:126 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:88343136-88344193	GM12891	blood:	n/a	n/a
2	MAX	chr4:88343270-88344313	ECC-1	luminal epithelium:	n/a	n/a
3	HCFC1	chr4:88342970-88344360	Hela-S3	cervix:	n/a	n/a
4	RELA	chr4:88343254-88344364	GM18951	blood:	n/a	n/a
5	POLR2A	chr4:88343285-88344281	HepG2	liver:	n/a	n/a
6	RELA	chr4:88343273-88344230	GM19099	blood:	n/a	n/a
7	POLR2A	chr4:88343068-88343948	K562	blood:	n/a	n/a
8	TAF1	chr4:88343212-88344217	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr4:88343230-88344271	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr4:88343005-88344214	IMR90	lung:	n/a	n/a
11	HCFC1	chr4:88343276-88344244	K562	blood:	n/a	n/a
12	RCOR1	chr4:88343269-88344266	K562	blood:	n/a	n/a
13	IRF1	chr4:88343229-88344212	K562	blood:	n/a	n/a
14	CBX3	chr4:88343234-88344300	K562	blood:	n/a	n/a
15	POLR2A	chr4:88343241-88344202	GM12892	blood:	n/a	n/a
16	POLR2A	chr4:88343244-88344308	GM12892	blood:	n/a	n/a
17	ZNF263	chr4:88343218-88344251	HEK293-T-REx	kidney:	n/a	n/a
18	POLR2A	chr4:88341808-88344299	GM12878	blood:	n/a	n/a
19	FOXM1	chr4:88342587-88344359	GM12878	blood:	n/a	n/a
20	POLR2A	chr4:88343258-88344198	GM12878	blood:	n/a	n/a
21	POLR2A	chr4:88343215-88344323	GM12892	blood:	n/a	n/a
22	TAF1	chr4:88343264-88344300	H1-hESC	embryonic stem cell:	n/a	n/a
23	CHD1	chr4:88343151-88344297	GM12878	blood:	n/a	n/a
24	POLR2A	chr4:88343258-88344201	GM12891	blood:	n/a	n/a
25	POLR2A	chr4:88343225-88344320	Raji	blood:	n/a	n/a
26	POLR2A	chr4:88343065-88344204	GM12878	blood:	n/a	n/a
27	SMARCB1	chr4:88343258-88344199	Hela-S3	cervix:	n/a	n/a
28	ATF2	chr4:88343287-88344133	GM12878	blood:	n/a	n/a
29	E2F6	chr4:88343217-88344270	A549	lung:	n/a	n/a
30	ZC3H11A	chr4:88343264-88344236	K562	blood:	n/a	n/a
31	POLR2A	chr4:88343216-88344275	HepG2	liver:	n/a	n/a
32	YY1	chr4:88343159-88343441	GM12878	blood:	n/a	n/a
33	POLR2A	chr4:88342959-88344255	GM12878	blood:	n/a	n/a
34	POLR2A	chr4:88342962-88344316	K562	blood:	n/a	n/a
35	POLR2A	chr4:88343211-88344230	H1-hESC	embryonic stem cell:	n/a	n/a
36	RAD21	chr4:88343259-88343725	HepG2	liver:	n/a	n/a
37	USF1	chr4:88343209-88344254	HCT-116	colon:	n/a	chr4:88343815-88343826
38	TCF12	chr4:88343228-88344369	A549	lung:	n/a	n/a
39	NR2F2	chr4:88343106-88344322	K562	blood:	n/a	n/a
40	USF2	chr4:88343242-88344118	GM12878	blood:	n/a	n/a
41	NFIC	chr4:88343086-88344244	GM12878	blood:	n/a	n/a
42	POLR2A	chr4:88343123-88344267	GM18951	blood:	n/a	n/a
43	POLR2A	chr4:88343287-88344194	K562	blood:	n/a	n/a
44	POLR2A	chr4:88343281-88344260	K562	blood:	n/a	n/a
45	POLR2A	chr4:88343229-88344361	SK-N-MC	brain:	n/a	n/a
46	POLR2A	chr4:88343240-88344261	GM12878	blood:	n/a	n/a
47	STAT5A	chr4:88343109-88344322	GM12878	blood:	n/a	chr4:88343136-88343144
48	MAX	chr4:88343155-88344295	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr4:88343288-88344103	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr4:88343153-88344199	HL-60	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:88310667..88314164-chr4:88342247..88345345,4	K562	blood:
2	chr4:88341987..88343662-chr4:88383872..88386006,2	MCF-7	breast:
3	chr4:88341784..88343437-chr4:88384944..88387219,2	K562	blood:
4	chr4:88333084..88334930-chr4:88342115..88343742,2	MCF-7	breast:
5	chr4:88339085..88341655-chr4:88342092..88343723,2	MCF-7	breast:
6	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
ENSG00000198189	Chromatin interaction
ENSG00000251716	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10000196	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10009948	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10023606	0.96[ASN][1000 genomes]
rs10024781	0.93[ASN][1000 genomes]
rs10030035	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10032122	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10084883	0.96[ASN][1000 genomes]
rs12640451	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12640894	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12648665	0.95[EUR][1000 genomes]
rs12650763	0.96[ASN][1000 genomes]
rs12651034	0.96[ASN][1000 genomes]
rs28366407	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28415220	0.92[ASN][1000 genomes]
rs28437709	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28493315	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28493566	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28529046	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28535549	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28696943	0.89[ASN][1000 genomes]
rs28712618	0.96[ASN][1000 genomes]
rs28718986	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28762371	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28805573	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34027531	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4411944	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56153912	0.98[ASN][1000 genomes]
rs58192677	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67121411	0.95[ASN][1000 genomes]
rs68045074	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72652067	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7665115	0.96[ASN][1000 genomes]
rs7673763	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7677249	0.96[ASN][1000 genomes]
rs7680878	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7690728	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9995987	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9998212	0.81[EUR][1000 genomes];0.98[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
rs55824708	HSD17B11	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88341400-88343400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:88342200-88343400	Flanking Active TSS	Liver	Liver
3	chr4:88342400-88344800	Active TSS	Brain Anterior Caudate	brain
4	chr4:88342400-88345400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:88342400-88345400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr4:88342600-88343400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:88342600-88343600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:88342600-88345000	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr4:88342600-88345400	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr4:88342600-88345400	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr4:88342600-88346000	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr4:88342800-88343400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr4:88342800-88343400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
14	chr4:88342800-88343400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:88342800-88343400	Flanking Active TSS	Brain Germinal Matrix	brain
16	chr4:88342800-88343400	Flanking Active TSS	Brain Substantia Nigra	brain
17	chr4:88342800-88343400	Flanking Active TSS	Colon Smooth Muscle	Colon
18	chr4:88342800-88343400	Flanking Active TSS	HepG2	liver
19	chr4:88342800-88343600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:88342800-88343600	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr4:88342800-88344800	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr4:88342800-88344800	Active TSS	Brain Hippocampus Middle	brain
23	chr4:88342800-88345000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:88342800-88345000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:88342800-88345000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:88342800-88345000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:88343000-88343400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:88343000-88343400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:88343000-88343400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr4:88343000-88343400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:88343000-88343400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr4:88343000-88343400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr4:88343000-88343400	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr4:88343000-88343400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr4:88343000-88343400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr4:88343000-88343400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr4:88343000-88343400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr4:88343000-88343400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr4:88343000-88343400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr4:88343000-88343400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:88343000-88343400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr4:88343000-88343400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr4:88343000-88343400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr4:88343000-88343400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr4:88343000-88343400	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr4:88343000-88343400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr4:88343000-88343400	Flanking Active TSS	Fetal Brain Male	brain
48	chr4:88343000-88343400	Flanking Active TSS	Fetal Brain Female	brain
49	chr4:88343000-88343400	Flanking Active TSS	Fetal Intestine Large	intestine
50	chr4:88343000-88343400	Flanking Active TSS	Fetal Muscle Leg	muscle

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