Variant report

Variant	rs58519566
Chromosome Location	chr5:74670429-74670430
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr5:74670198-74670581	HepG2	liver:	n/a	n/a
2	MAZ	chr5:74670341-74670492	HepG2	liver:	n/a	n/a
3	BHLHE40	chr5:74670189-74670530	HepG2	liver:	n/a	n/a
4	POLR2A	chr5:74669712-74670542	HepG2	liver:	n/a	n/a
5	EP300	chr5:74669819-74670564	HepG2	liver:	n/a	n/a
6	TCF7L2	chr5:74670220-74670649	HCT-116	colon:	n/a	n/a
7	EP300	chr5:74670202-74670582	HepG2	liver:	n/a	n/a
8	TBP	chr5:74670347-74670447	HepG2	liver:	n/a	n/a
9	MAX	chr5:74670091-74670636	HepG2	liver:	n/a	n/a
10	MXI1	chr5:74670221-74670527	HepG2	liver:	n/a	n/a
11	BHLHE40	chr5:74670215-74670528	HepG2	liver:	n/a	n/a
12	SP1	chr5:74670225-74670642	HepG2	liver:	n/a	n/a
13	FOXA2	chr5:74670250-74670512	HepG2	liver:	n/a	n/a
14	EP300	chr5:74670244-74670618	HepG2	liver:	n/a	n/a
15	MAX	chr5:74670215-74670577	HepG2	liver:	n/a	n/a
16	SMC3	chr5:74670346-74670595	HepG2	liver:	n/a	n/a
17	TCF7L2	chr5:74669804-74670898	HepG2	liver:	n/a	n/a
18	NR2F2	chr5:74670176-74670645	HepG2	liver:	n/a	n/a
19	FOXA1	chr5:74670165-74670584	HepG2	liver:	n/a	n/a
20	CEBPB	chr5:74670284-74670592	HepG2	liver:	n/a	chr5:74670514-74670525
21	ARID3A	chr5:74669706-74670670	HepG2	liver:	n/a	n/a
22	BHLHE40	chr5:74669765-74670604	HepG2	liver:	n/a	n/a
23	CEBPB	chr5:74670404-74670578	HepG2	liver:	n/a	chr5:74670514-74670525
24	CEBPB	chr5:74670343-74670685	HepG2	liver:	n/a	chr5:74670514-74670525
25	CEBPB	chr5:74670274-74670718	HepG2	liver:	n/a	chr5:74670514-74670525
26	MAX	chr5:74669953-74670502	HepG2	liver:	n/a	n/a
27	FOXA1	chr5:74670203-74670553	HepG2	liver:	n/a	n/a
28	USF2	chr5:74670234-74670439	HepG2	liver:	n/a	n/a
29	JUND	chr5:74670383-74670574	HepG2	liver:	n/a	n/a
30	FOXA1	chr5:74670184-74670619	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74631027..74633689-chr5:74669899..74673257,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HMGCR-2	chr5:74670288-74670634	NONHSAT102207

No data

Variant related genes	Relation type
COL4A3BP	TF binding region
ENSG00000113161	Chromatin interaction
ENSG00000247372	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10038945	0.89[EUR][1000 genomes]
rs10041470	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10055011	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10059022	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10061689	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10067900	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10076819	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10077427	0.93[EUR][1000 genomes]
rs10474437	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12173076	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13360099	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13361353	0.93[EUR][1000 genomes]
rs1469051	0.85[EUR][1000 genomes]
rs1553234	0.93[EUR][1000 genomes]
rs1909719	0.93[EUR][1000 genomes]
rs28408106	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28612248	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28874007	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3804231	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4703671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4704213	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56859362	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5744544	0.88[EUR][1000 genomes]
rs5744545	0.86[EUR][1000 genomes]
rs5744636	0.93[EUR][1000 genomes]
rs5744667	0.87[EUR][1000 genomes]
rs5744704	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs5744709	0.88[EUR][1000 genomes]
rs5744712	0.88[EUR][1000 genomes]
rs61303403	0.81[EUR][1000 genomes]
rs6891560	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72633963	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72633964	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72633965	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72633966	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72633967	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72633968	0.90[EUR][1000 genomes]
rs72633969	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72633970	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72633971	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72633972	0.91[EUR][1000 genomes]
rs72633973	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs72633974	0.93[EUR][1000 genomes]
rs7356633	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7726478	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9293652	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9293654	0.88[EUR][1000 genomes]
rs9293655	0.91[EUR][1000 genomes]
rs979182	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882192	chr5:74641707-74707762	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv980685	chr5:74669881-74670738	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74656400-74673600	Weak transcription	Psoas Muscle	Psoas
2	chr5:74656400-74673600	Weak transcription	Small Intestine	intestine
3	chr5:74656400-74673600	Weak transcription	Spleen	Spleen
4	chr5:74656400-74674000	Weak transcription	Brain Germinal Matrix	brain
5	chr5:74656400-74674800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr5:74656400-74674800	Weak transcription	Brain Substantia Nigra	brain
7	chr5:74656400-74676800	Weak transcription	Fetal Brain Male	brain
8	chr5:74656400-74687200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:74656400-74725600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr5:74656600-74670600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr5:74656600-74675600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:74656600-74675800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:74656600-74675800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr5:74656600-74676800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr5:74656600-74677200	Weak transcription	Aorta	Aorta
16	chr5:74656600-74694800	Weak transcription	Brain Angular Gyrus	brain
17	chr5:74656800-74676200	Weak transcription	Colonic Mucosa	Colon
18	chr5:74656800-74731400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr5:74657400-74674800	Weak transcription	A549	lung
20	chr5:74657600-74673600	Weak transcription	Lung	lung
21	chr5:74657800-74708000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr5:74658000-74674800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr5:74658400-74673200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr5:74658600-74673200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr5:74658600-74674800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr5:74658600-74674800	Weak transcription	Fetal Kidney	kidney
27	chr5:74659000-74674600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr5:74659200-74674800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:74659600-74673600	Weak transcription	Esophagus	oesophagus
30	chr5:74659600-74673600	Weak transcription	Gastric	stomach
31	chr5:74659600-74675800	Weak transcription	Brain Hippocampus Middle	brain
32	chr5:74659800-74673600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr5:74659800-74677000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr5:74659800-74684800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr5:74659800-74720600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr5:74660000-74674600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr5:74660000-74722800	Weak transcription	Fetal Heart	heart
38	chr5:74660200-74673600	Weak transcription	Fetal Muscle Leg	muscle
39	chr5:74660200-74707800	Weak transcription	Stomach Mucosa	stomach
40	chr5:74660400-74673600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:74661800-74683600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:74663200-74676800	Weak transcription	K562	blood
43	chr5:74664600-74670600	Weak transcription	Osteobl	bone
44	chr5:74664600-74674400	Weak transcription	NH-A	brain
45	chr5:74664600-74674600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr5:74664600-74676800	Weak transcription	NHLF	lung
47	chr5:74664600-74677000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr5:74664800-74670800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr5:74664800-74677000	Weak transcription	HUVEC	blood vessel
50	chr5:74665000-74703000	Strong transcription	Primary monocytes fromperipheralblood	blood

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