Variant report

Variant	rs56994557
Chromosome Location	chr11:62569572-62569573
allele	A/G
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	POLR2A	chr11:62568742-62569593	K562	blood:	n/a	n/a
2	POLR2A	chr11:62568636-62569599	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:62568236-62569814	GM12878	blood:	n/a	n/a
4	SPI1	chr11:62569380-62569649	GM12891	blood:	n/a	n/a
5	EBF1	chr11:62569536-62569609	GM12878	blood:	n/a	chr11:62569557-62569568
6	BATF	chr11:62569392-62569668	GM12878	blood:	n/a	n/a
7	POLR2A	chr11:62569163-62569772	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:62565367..62576307-chr11:62617328..62626616,39	K562	blood:
2	chr11:62358215..62361190-chr11:62569453..62571733,2	K562	blood:
3	chr11:62568262..62574296-chr11:62646831..62652869,25	K562	blood:

Variant related genes	Relation type
NXF1	TF binding region
ENSG00000255508	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000255717	Chromatin interaction
ENSG00000149016	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11231220	1.00[AMR][1000 genomes]
rs11231261	0.86[AFR][1000 genomes]
rs12270342	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12288417	1.00[AMR][1000 genomes]
rs12290152	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12292281	1.00[AMR][1000 genomes]
rs12295052	1.00[AMR][1000 genomes]
rs12295516	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28400288	1.00[AMR][1000 genomes]
rs58003814	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58505493	1.00[AMR][1000 genomes]
rs58792209	1.00[AMR][1000 genomes]
rs59143369	1.00[AMR][1000 genomes]
rs61088491	1.00[AMR][1000 genomes]
rs73483955	1.00[AMR][1000 genomes]
rs73483965	1.00[AMR][1000 genomes]
rs73483978	1.00[AMR][1000 genomes]
rs73485621	1.00[AMR][1000 genomes]
rs73485634	1.00[AMR][1000 genomes]
rs73485689	1.00[AMR][1000 genomes]
rs73487820	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73487823	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73487824	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73487852	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73487868	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73502144	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1401 gene(s)	inside rSNPs	diseases
4	nsv497903	chr11:62330308-62608042	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	489 gene(s)	inside rSNPs	diseases
5	nsv897623	chr11:62438819-62603916	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	215 gene(s)	inside rSNPs	diseases
6	nsv508636	chr11:62547114-62644458	Transcr. at gene 5' and 3' Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1195 gene(s)	inside rSNPs	diseases
7	nsv1051308	chr11:62564713-62673136	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1199 gene(s)	inside rSNPs	diseases
8	nsv541058	chr11:62564713-62673136	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1199 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62559400-62571200	Genic enhancers	Placenta	Placenta
2	chr11:62559400-62572000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:62559800-62571400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr11:62560000-62570400	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr11:62560000-62571000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr11:62560000-62571200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:62560000-62571400	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr11:62560000-62571400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr11:62560200-62569800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:62560200-62570000	Strong transcription	Right Ventricle	heart
11	chr11:62560200-62570200	Strong transcription	Esophagus	oesophagus
12	chr11:62560200-62570200	Strong transcription	NHDF-Ad	bronchial
13	chr11:62560200-62570400	Strong transcription	Brain Angular Gyrus	brain
14	chr11:62560200-62570400	Strong transcription	Colonic Mucosa	Colon
15	chr11:62560200-62570800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:62560200-62570800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:62560200-62570800	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr11:62560200-62570800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr11:62560200-62570800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr11:62560200-62570800	Strong transcription	Placenta Amnion	Placenta Amnion
21	chr11:62560200-62570800	Strong transcription	Spleen	Spleen
22	chr11:62560200-62571000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:62560200-62571000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr11:62560200-62571000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:62560200-62571000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr11:62560200-62571000	Strong transcription	Adipose Nuclei	Adipose
27	chr11:62560200-62571000	Strong transcription	Liver	Liver
28	chr11:62560200-62571000	Strong transcription	Brain Anterior Caudate	brain
29	chr11:62560200-62571000	Strong transcription	Brain Cingulate Gyrus	brain
30	chr11:62560200-62571000	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr11:62560200-62571000	Strong transcription	Brain Substantia Nigra	brain
32	chr11:62560200-62571000	Strong transcription	Fetal Thymus	thymus
33	chr11:62560200-62571000	Strong transcription	Lung	lung
34	chr11:62560200-62571000	Strong transcription	Thymus	Thymus
35	chr11:62560200-62571000	Strong transcription	HUVEC	blood vessel
36	chr11:62560200-62571000	Strong transcription	NH-A	brain
37	chr11:62560200-62571000	Strong transcription	Osteobl	bone
38	chr11:62560200-62571200	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr11:62560200-62571200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr11:62560200-62571200	Strong transcription	Brain Germinal Matrix	brain
41	chr11:62560200-62571200	Strong transcription	Left Ventricle	heart
42	chr11:62560200-62571200	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr11:62560200-62571200	Strong transcription	A549	lung
44	chr11:62560200-62571200	Strong transcription	HSMMtube	muscle
45	chr11:62560200-62571200	Strong transcription	NHEK	skin
46	chr11:62560200-62571400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr11:62560200-62571400	Strong transcription	Fetal Muscle Trunk	muscle
48	chr11:62560400-62569800	Strong transcription	HepG2	liver
49	chr11:62560400-62570000	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr11:62560400-62570200	Strong transcription	Brain Hippocampus Middle	brain

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