Variant report

Variant	rs11249655
Chromosome Location	chr5:179111290-179111291
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr5:179110625-179111549	HepG2	liver:	n/a	n/a
2	ARID3A	chr5:179110890-179111299	HepG2	liver:	n/a	n/a
3	FOXA1	chr5:179110794-179111409	HepG2	liver:	n/a	chr5:179111089-179111104
4	SP1	chr5:179110868-179111329	HepG2	liver:	n/a	n/a
5	FOXA1	chr5:179110824-179111346	T-47D	breast:	n/a	chr5:179111089-179111104
6	FOXA2	chr5:179110903-179111293	HepG2	liver:	n/a	n/a
7	FOXA1	chr5:179110820-179111357	HepG2	liver:	n/a	chr5:179111089-179111104
8	NFIC	chr5:179110798-179111323	HepG2	liver:	n/a	n/a
9	FOXA1	chr5:179110798-179111399	HepG2	liver:	n/a	chr5:179111089-179111104
10	FOXA1	chr5:179110888-179111473	HepG2	liver:	n/a	chr5:179111089-179111104
11	FOXA2	chr5:179110885-179111394	A549	lung:	n/a	n/a
12	ZNF384	chr5:179111279-179111430	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:179104126..179107921-chr5:179108631..179111977,3	K562	blood:
2	chr5:179101603..179111989-chr5:179122927..179129527,32	MCF-7	breast:
3	chr5:179110444..179112738-chr5:179123808..179127220,5	MCF-7	breast:
4	chr5:179105005..179107336-chr5:179108581..179112647,5	MCF-7	breast:

Variant related genes	Relation type
CBY3	TF binding region
ENSG00000225051	Chromatin interaction
ENSG00000127022	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11249656	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11249657	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11249658	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11749559	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11750523	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12188238	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12515399	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12518476	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28674071	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28846185	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55702506	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56159807	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60216315	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62406697	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62406698	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67484565	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6879412	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7719302	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9637934	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9637935	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9763971	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][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	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179106400-179118200	Weak transcription	Right Ventricle	heart
2	chr5:179106600-179112600	Weak transcription	Brain Anterior Caudate	brain
3	chr5:179106600-179113600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr5:179106600-179124200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:179106600-179124800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr5:179106800-179123000	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:179107400-179121400	Weak transcription	Primary B cells from cord blood	blood
8	chr5:179107600-179117600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr5:179107600-179119600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr5:179107600-179123200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:179107600-179123200	Weak transcription	Fetal Thymus	thymus
12	chr5:179107600-179123400	Weak transcription	Fetal Intestine Small	intestine
13	chr5:179107800-179114400	Weak transcription	Spleen	Spleen
14	chr5:179108000-179115600	Weak transcription	Brain Substantia Nigra	brain
15	chr5:179108400-179123000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:179108600-179112400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:179108600-179123600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr5:179109800-179111800	Enhancers	HepG2	liver
19	chr5:179110800-179111400	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr5:179110800-179111600	Enhancers	GM12878-XiMat	blood
21	chr5:179111000-179111400	Enhancers	Liver	Liver
22	chr5:179111000-179111400	Enhancers	Stomach Mucosa	stomach
23	chr5:179111200-179111400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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