Variant report

Variant	rs68045074
Chromosome Location	chr4:88343524-88343525
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:413)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:413 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF7	chr4:88343380-88344281	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr4:88343136-88344193	GM12891	blood:	n/a	n/a
3	HEY1	chr4:88343296-88344271	HepG2	liver:	n/a	n/a
4	POLR2A	chr4:88343432-88343989	HepG2	liver:	n/a	n/a
5	CTCF	chr4:88343400-88343550	AG09319	gingival:	n/a	n/a
6	EP300	chr4:88343512-88344192	GM12878	blood:	n/a	chr4:88343593-88343607
7	MAX	chr4:88343270-88344313	ECC-1	luminal epithelium:	n/a	n/a
8	NFIC	chr4:88343414-88344040	HepG2	liver:	n/a	n/a
9	CREB1	chr4:88343394-88344201	K562	blood:	n/a	n/a
10	ZNF143	chr4:88343389-88344188	GM12878	blood:	n/a	n/a
11	BHLHE40	chr4:88343407-88344493	GM12878	blood:	n/a	n/a
12	SPI1	chr4:88343500-88343767	K562	blood:	n/a	n/a
13	JUND	chr4:88343383-88344353	K562	blood:	n/a	n/a
14	HCFC1	chr4:88342970-88344360	Hela-S3	cervix:	n/a	n/a
15	RELA	chr4:88343254-88344364	GM18951	blood:	n/a	n/a
16	POLR2A	chr4:88343285-88344281	HepG2	liver:	n/a	n/a
17	RELA	chr4:88343273-88344230	GM19099	blood:	n/a	n/a
18	TAF1	chr4:88343442-88344146	Hela-S3	cervix:	n/a	n/a
19	SIN3AK20	chr4:88343313-88344252	MCF-7	breast:	n/a	n/a
20	ELF1	chr4:88343475-88343834	A549	lung:	n/a	n/a
21	RCOR1	chr4:88343386-88344100	GM12878	blood:	n/a	n/a
22	MYC	chr4:88343385-88344266	K562	blood:	n/a	n/a
23	NFIC	chr4:88343305-88344141	ECC-1	luminal epithelium:	n/a	n/a
24	SIN3AK20	chr4:88343469-88344120	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr4:88343068-88343948	K562	blood:	n/a	n/a
26	POLR2A	chr4:88343362-88344172	A549	lung:	n/a	n/a
27	POLR2A	chr4:88343355-88344215	HepG2	liver:	n/a	n/a
28	POLR2A	chr4:88343402-88344227	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr4:88343380-88343530	GM12871	blood:	n/a	n/a
30	ATF2	chr4:88343477-88344011	H1-hESC	embryonic stem cell:	n/a	n/a
31	TAF1	chr4:88343212-88344217	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr4:88343230-88344271	ECC-1	luminal epithelium:	n/a	n/a
33	GATA3	chr4:88343394-88344271	SK-N-SH	brain:	n/a	chr4:88343602-88343612
34	TCF12	chr4:88343458-88344030	A549	lung:	n/a	n/a
35	EP300	chr4:88343453-88344273	K562	blood:	n/a	chr4:88343593-88343607
36	RCOR1	chr4:88343422-88344214	K562	blood:	n/a	n/a
37	YY1	chr4:88343500-88344239	HCT-116	colon:	n/a	chr4:88343649-88343663
38	POLR2A	chr4:88343005-88344214	IMR90	lung:	n/a	n/a
39	NR2F2	chr4:88343355-88344064	K562	blood:	n/a	n/a
40	HCFC1	chr4:88343276-88344244	K562	blood:	n/a	n/a
41	RCOR1	chr4:88343269-88344266	K562	blood:	n/a	n/a
42	POLR2A	chr4:88343332-88344241	HCT-116	colon:	n/a	n/a
43	TAF1	chr4:88343481-88344158	GM12891	blood:	n/a	n/a
44	POLR2A	chr4:88343324-88344162	ProgFib	skin:	n/a	n/a
45	CTCF	chr4:88343520-88343670	NHDF-neo	bronchial:	n/a	n/a
46	SIX5	chr4:88343356-88343888	A549	lung:	n/a	n/a
47	GATA3	chr4:88343439-88344250	MCF-7	breast:	n/a	chr4:88343602-88343612
48	CREB1	chr4:88343319-88344311	HepG2	liver:	n/a	n/a
49	TBL1XR1	chr4:88343493-88344107	GM12878	blood:	n/a	n/a
50	NFATC1	chr4:88343346-88344297	GM12878	blood:	n/a	n/a

No data

(count:5 , 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	chr4:88333084..88334930-chr4:88342115..88343742,2	MCF-7	breast:
4	chr4:88339085..88341655-chr4:88342092..88343723,2	MCF-7	breast:
5	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: 0)

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

rs_ID	r²[population]
rs10000196	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10009948	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10023606	0.96[ASN][1000 genomes]
rs10024781	0.93[ASN][1000 genomes]
rs10030035	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10032122	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10084883	0.96[ASN][1000 genomes]
rs12640451	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12640894	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12648665	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12650763	0.96[ASN][1000 genomes]
rs12651034	0.96[ASN][1000 genomes]
rs28366407	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28415220	0.92[ASN][1000 genomes]
rs28437709	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28493315	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28493566	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28529046	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28535549	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28696943	0.89[ASN][1000 genomes]
rs28712618	0.96[ASN][1000 genomes]
rs28718986	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28762371	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28805573	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34027531	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4411944	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55824708	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56153912	0.98[ASN][1000 genomes]
rs58192677	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67121411	0.95[ASN][1000 genomes]
rs72652067	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7665115	0.96[ASN][1000 genomes]
rs7673763	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7677249	0.96[ASN][1000 genomes]
rs7680878	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7690728	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9995987	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9998212	0.83[AMR][1000 genomes];0.80[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

No data

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	chr4:88342600-88343600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:88342600-88345000	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr4:88342600-88345400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr4:88342600-88345400	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr4:88342600-88346000	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr4:88342800-88343600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:88342800-88343600	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr4:88342800-88344800	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr4:88342800-88344800	Active TSS	Brain Hippocampus Middle	brain
13	chr4:88342800-88345000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:88342800-88345000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:88342800-88345000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:88342800-88345000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:88343000-88343600	Flanking Active TSS	Fetal Intestine Small	intestine
18	chr4:88343000-88343600	Flanking Active TSS	Fetal Lung	lung
19	chr4:88343000-88343600	Flanking Active TSS	Fetal Muscle Trunk	muscle
20	chr4:88343000-88343600	Flanking Active TSS	Hela-S3	cervix
21	chr4:88343000-88343800	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr4:88343000-88344400	Active TSS	Esophagus	oesophagus
23	chr4:88343000-88344600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr4:88343000-88344600	Active TSS	Osteobl	bone
25	chr4:88343000-88344800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:88343000-88344800	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr4:88343000-88344800	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr4:88343000-88344800	Active TSS	Rectal Smooth Muscle	rectum
29	chr4:88343000-88344800	Active TSS	A549	lung
30	chr4:88343000-88344800	Active TSS	HMEC	breast
31	chr4:88343000-88344800	Active TSS	NHEK	skin
32	chr4:88343000-88345000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:88343000-88345000	Active TSS	Colonic Mucosa	Colon
34	chr4:88343000-88345000	Active TSS	HSMMtube	muscle
35	chr4:88343000-88345000	Active TSS	NHDF-Ad	bronchial
36	chr4:88343000-88345200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:88343000-88345200	Active TSS	NHLF	lung
38	chr4:88343000-88345400	Active TSS	H9 Cell Line	embryonic stem cell
39	chr4:88343000-88345400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr4:88343000-88345400	Active TSS	Ovary	ovary
41	chr4:88343000-88345800	Active TSS	HSMM	muscle
42	chr4:88343200-88343600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:88343200-88343600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr4:88343200-88343600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:88343200-88343600	Flanking Active TSS	Placenta	Placenta
46	chr4:88343200-88343600	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr4:88343200-88344200	Active TSS	Primary T cells from cord blood	blood
48	chr4:88343200-88344400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:88343200-88344400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr4:88343200-88344400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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