Variant report

Variant	rs56023844
Chromosome Location	chr4:16217627-16217628
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	POLR2A	chr4:16217489-16218963	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:16217606-16218482	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:16216932..16218804-chr4:16227245..16229857,2	MCF-7	breast:
2	chr4:16212529..16219737-chr4:16225844..16229602,8	MCF-7	breast:

Variant related genes	Relation type
TAPT1	TF binding region
ENSG00000263327	Chromatin interaction
ENSG00000169762	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10516298	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10939653	0.84[ASN][1000 genomes]
rs11724076	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11724423	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11724467	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11731602	0.83[ASN][1000 genomes]
rs11736424	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11736827	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12504884	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12506478	0.93[ASN][1000 genomes]
rs12513244	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12643544	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12645055	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12651110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1373112	0.84[ASN][1000 genomes]
rs1662652	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16893099	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16893119	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16893138	0.83[ASN][1000 genomes]
rs16893143	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16893144	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16893147	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16893158	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs317874	0.82[ASN][1000 genomes]
rs35851218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56218994	0.83[ASN][1000 genomes]
rs57089965	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58047733	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60460559	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60768295	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73128422	0.91[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs73128457	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73130433	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73130439	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73130445	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73130449	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130451	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130453	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130456	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7657191	0.81[ASN][1000 genomes]
rs894639	0.88[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	nsv998299	chr4:16031459-16226466	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16181200-16223800	Weak transcription	Fetal Brain Male	brain
2	chr4:16193000-16225800	Weak transcription	Colonic Mucosa	Colon
3	chr4:16193200-16225800	Weak transcription	Fetal Brain Female	brain
4	chr4:16198600-16221200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:16198600-16222400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:16198800-16218800	Weak transcription	HSMM	muscle
7	chr4:16198800-16225600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:16198800-16226000	Weak transcription	NHEK	skin
9	chr4:16198800-16226400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:16200800-16218000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr4:16202800-16220800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:16204800-16226600	Weak transcription	NH-A	brain
13	chr4:16205200-16225600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:16206400-16218400	Weak transcription	Fetal Lung	lung
15	chr4:16206600-16218400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:16207400-16223600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:16208400-16219000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr4:16208400-16224400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:16208400-16225200	Weak transcription	Fetal Kidney	kidney
20	chr4:16208400-16225800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:16208800-16225600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:16208800-16225600	Weak transcription	Esophagus	oesophagus
23	chr4:16208800-16225600	Weak transcription	Gastric	stomach
24	chr4:16208800-16225800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:16208800-16225800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr4:16208800-16227200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr4:16209000-16225600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:16209200-16223400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:16209200-16225600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:16209200-16225600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr4:16209400-16226200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:16209400-16226200	Weak transcription	HSMMtube	muscle
33	chr4:16209600-16221400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:16210400-16225800	Weak transcription	Brain Germinal Matrix	brain
35	chr4:16212000-16217800	Weak transcription	Aorta	Aorta
36	chr4:16212000-16220600	Weak transcription	A549	lung
37	chr4:16212200-16226000	Weak transcription	NHDF-Ad	bronchial
38	chr4:16213000-16221400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr4:16214000-16218800	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr4:16214000-16218800	Weak transcription	Brain Substantia Nigra	brain
41	chr4:16214000-16224400	Weak transcription	Brain Anterior Caudate	brain
42	chr4:16214200-16219000	Weak transcription	HUVEC	blood vessel
43	chr4:16214200-16221800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr4:16214200-16224200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:16214400-16217800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr4:16214400-16218400	Weak transcription	Fetal Intestine Small	intestine
47	chr4:16214400-16218600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:16214400-16218600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr4:16214400-16220800	Weak transcription	Fetal Stomach	stomach
50	chr4:16214400-16226800	Weak transcription	Fetal Muscle Trunk	muscle

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