Variant report

Variant	rs2139414
Chromosome Location	chr6:114490091-114490092
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	HEY1	chr6:114490073-114490352	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:114489134-114490792	HepG2	liver:	n/a	n/a
3	FOXA2	chr6:114488420-114490241	HepG2	liver:	n/a	chr6:114489670-114489682 chr6:114489205-114489217 chr6:114489674-114489686
4	NFIC	chr6:114488464-114490098	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:114489296-114490175	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
HS3ST5	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10782179	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1401774	0.88[ASN][1000 genomes]
rs1519690	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2349211	0.96[ASN][1000 genomes]
rs4945993	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6915954	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6928606	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6936717	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7746324	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7751951	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7766866	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs908936	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs925981	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs925982	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs925983	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs928606	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9320481	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9320482	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9320483	0.96[ASN][1000 genomes]
rs9320486	0.88[ASN][1000 genomes]
rs9372389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9372390	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9374441	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9374443	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9387194	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9387195	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9387196	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9400698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9400699	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9400700	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9400701	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9400702	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9400703	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9481426	0.88[ASN][1000 genomes]
rs9481430	0.88[ASN][1000 genomes]
rs9481433	0.88[ASN][1000 genomes]
rs9488340	0.88[ASN][1000 genomes]
rs9488343	0.88[ASN][1000 genomes]
rs984769	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024062	chr6:114311029-114679557	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
2	nsv1034897	chr6:114454186-114555679	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv34434	chr6:114465305-115462799	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1029370	chr6:114471446-114566884	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv464024	chr6:114489321-114837181	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv604544	chr6:114489321-114837181	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114476200-114493600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:114476200-114497800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:114477000-114491800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:114485000-114491200	Enhancers	Fetal Intestine Small	intestine
5	chr6:114485400-114497800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr6:114485600-114490200	Enhancers	Fetal Intestine Large	intestine
7	chr6:114488200-114490800	Enhancers	Brain Anterior Caudate	brain
8	chr6:114488600-114490800	Enhancers	Brain Hippocampus Middle	brain
9	chr6:114488600-114491800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:114488800-114490600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr6:114489000-114491200	Enhancers	Stomach Mucosa	stomach
12	chr6:114489000-114496600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr6:114489200-114492200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:114489600-114490600	Weak transcription	Brain Substantia Nigra	brain
15	chr6:114489600-114490600	Weak transcription	Gastric	stomach
16	chr6:114489800-114491000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:114489800-114493400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:114489800-114494000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:114489800-114495200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:114490000-114490600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr6:114490000-114490600	Weak transcription	Fetal Lung	lung
22	chr6:114490000-114491200	Flanking Active TSS	HepG2	liver
23	chr6:114490000-114493600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr6:114490000-114502800	Weak transcription	Brain Inferior Temporal Lobe	brain

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