Variant report

Variant	rs56129345
Chromosome Location	chr2:20791002-20791003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:20790156-20791282	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:20788236-20791253	HepG2	liver:	n/a	n/a
3	HEY1	chr2:20788217-20791446	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:20789823-20791179	HepG2	liver:	n/a	n/a
5	HEY1	chr2:20790965-20791325	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:20789971-20791121	HepG2	liver:	n/a	n/a
7	POLR2A	chr2:20790907-20792069	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:20788190-20791944	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20644797..20655251-chr2:20787626..20802274,53	MCF-7	breast:
2	chr2:20790147..20792298-chr2:20794346..20796797,2	K562	blood:
3	chr2:20783982..20787771-chr2:20790367..20794656,9	K562	blood:
4	chr2:20786032..20787852-chr2:20789540..20791867,2	K562	blood:
5	chr2:20644186..20651576-chr2:20790196..20799394,18	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C2orf43-1	chr2:20790535-20791007	ENSG00000231948.2
2	lnc-GDF7-4	chr2:20790535-20791007	NONHSAT069453

No data

Variant related genes	Relation type
ENSG00000269976	TF binding region
ENSG00000143878	Chromatin interaction
ENSG00000228950	Chromatin interaction
ENSG00000269976	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10166792	0.94[ASN][1000 genomes]
rs10177787	0.94[ASN][1000 genomes]
rs10190705	0.90[ASN][1000 genomes]
rs10195324	0.89[ASN][1000 genomes]
rs10195722	0.84[ASN][1000 genomes]
rs10200207	0.89[ASN][1000 genomes]
rs11096677	0.94[ASN][1000 genomes]
rs1123781	0.95[ASN][1000 genomes]
rs11691255	0.90[ASN][1000 genomes]
rs11897611	0.84[ASN][1000 genomes]
rs12472478	0.84[ASN][1000 genomes]
rs12621527	0.84[ASN][1000 genomes]
rs13422371	0.90[ASN][1000 genomes]
rs16987857	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16987878	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16987880	0.94[ASN][1000 genomes]
rs16987884	0.90[ASN][1000 genomes]
rs2882035	0.94[ASN][1000 genomes]
rs2882036	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4666315	0.94[ASN][1000 genomes]
rs4666429	0.94[ASN][1000 genomes]
rs4666430	0.84[ASN][1000 genomes]
rs4666431	0.84[ASN][1000 genomes]
rs55835545	0.94[ASN][1000 genomes]
rs59169527	0.89[ASN][1000 genomes]
rs72782365	0.99[ASN][1000 genomes]
rs72782367	0.93[ASN][1000 genomes]
rs72782368	0.94[ASN][1000 genomes]
rs766474	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs921601	0.94[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	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1012037	chr2:20770850-20824893	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535598	chr2:20770850-20824893	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20784600-20794200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:20785000-20796000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr2:20785800-20793000	Weak transcription	Gastric	stomach
4	chr2:20785800-20794600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:20785800-20795200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr2:20785800-20796000	Weak transcription	Aorta	Aorta
7	chr2:20786000-20792200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:20786000-20792800	Weak transcription	Colonic Mucosa	Colon
9	chr2:20786000-20793000	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:20786000-20794200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:20786000-20795200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:20786200-20797600	Weak transcription	Psoas Muscle	Psoas
13	chr2:20786800-20793400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr2:20787200-20800200	Enhancers	Right Ventricle	heart
15	chr2:20787400-20792800	Weak transcription	Fetal Kidney	kidney
16	chr2:20787400-20794800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:20788200-20792000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr2:20788400-20791200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:20788400-20791400	Enhancers	Right Atrium	heart
20	chr2:20788400-20791800	Enhancers	Left Ventricle	heart
21	chr2:20788400-20794200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:20788400-20794200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:20788600-20791600	Enhancers	Muscle Satellite Cultured Cells	--
24	chr2:20788800-20791400	Enhancers	Fetal Muscle Leg	muscle
25	chr2:20788800-20791400	Enhancers	Fetal Stomach	stomach
26	chr2:20788800-20791400	Enhancers	NHDF-Ad	bronchial
27	chr2:20788800-20791600	Enhancers	HSMM	muscle
28	chr2:20789000-20791400	Enhancers	NHLF	lung
29	chr2:20789000-20794000	Enhancers	NHEK	skin
30	chr2:20789000-20798200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:20789200-20791400	Enhancers	HSMMtube	muscle
32	chr2:20789200-20797000	Enhancers	Spleen	Spleen
33	chr2:20789200-20800400	Enhancers	Placenta	Placenta
34	chr2:20789400-20791200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:20789400-20791800	Weak transcription	K562	blood
36	chr2:20789400-20795400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:20789600-20792800	Weak transcription	HUVEC	blood vessel
38	chr2:20790000-20791200	Enhancers	Esophagus	oesophagus
39	chr2:20790000-20792800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr2:20790200-20791200	Enhancers	Fetal Heart	heart
41	chr2:20790200-20791800	Enhancers	Ovary	ovary
42	chr2:20790200-20797800	Enhancers	Fetal Intestine Large	intestine
43	chr2:20790400-20791200	Enhancers	Colon Smooth Muscle	Colon
44	chr2:20790400-20791400	Flanking Active TSS	Liver	Liver
45	chr2:20790400-20791400	Enhancers	Brain Germinal Matrix	brain
46	chr2:20790400-20791400	Enhancers	Fetal Lung	lung
47	chr2:20790400-20791400	Enhancers	Rectal Smooth Muscle	rectum
48	chr2:20790400-20791600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:20790400-20792400	Weak transcription	A549	lung
50	chr2:20790400-20793600	Enhancers	Fetal Intestine Small	intestine

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