Variant report

Variant	rs55948553
Chromosome Location	chr5:112241507-112241508
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	chr5:112241461-112241659	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112195332..112197808-chr5:112240725..112243513,2	K562	blood:

Variant related genes	Relation type
ENSG00000266499	TF binding region
ENSG00000272869	Chromatin interaction
ENSG00000153037	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs56029122	1.00[AMR][1000 genomes]
rs59028501	0.84[AFR][1000 genomes]
rs59063648	0.84[AFR][1000 genomes]
rs60696542	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73789225	0.84[AFR][1000 genomes]
rs73789235	0.84[AFR][1000 genomes]
rs73789237	0.84[AFR][1000 genomes]
rs73789238	0.84[AFR][1000 genomes]
rs73789242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73789268	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv870231	chr5:112192379-112247084	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1029595	chr5:112197662-112242375	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1030103	chr5:112197662-112255712	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv537863	chr5:112197662-112255712	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112200600-112242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:112206400-112242800	Weak transcription	Fetal Brain Male	brain
3	chr5:112211600-112256400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:112212200-112256400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr5:112212600-112251400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr5:112215200-112255800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:112215800-112247200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:112221800-112256600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:112222000-112256400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:112223000-112243000	Weak transcription	Right Ventricle	heart
11	chr5:112223000-112245200	Weak transcription	Colonic Mucosa	Colon
12	chr5:112223000-112245200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr5:112223000-112256400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:112223000-112256600	Weak transcription	Thymus	Thymus
15	chr5:112224800-112242400	Weak transcription	Right Atrium	heart
16	chr5:112224800-112250600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr5:112225000-112251600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr5:112228600-112242400	Weak transcription	Spleen	Spleen
19	chr5:112229600-112250000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr5:112229600-112256600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:112230200-112251600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr5:112232000-112242800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:112232200-112242200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr5:112232200-112242200	Weak transcription	HepG2	liver
25	chr5:112232600-112242800	Weak transcription	Pancreas	Pancrea
26	chr5:112232600-112250200	Weak transcription	Stomach Mucosa	stomach
27	chr5:112232800-112242800	Weak transcription	Brain Substantia Nigra	brain
28	chr5:112233600-112246600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr5:112234200-112249400	Weak transcription	Fetal Heart	heart
30	chr5:112234400-112242800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr5:112234600-112246400	Weak transcription	HMEC	breast
32	chr5:112235200-112245200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr5:112235600-112242800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr5:112236400-112245200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr5:112236400-112245600	Weak transcription	Esophagus	oesophagus
36	chr5:112237000-112244600	Weak transcription	NHDF-Ad	bronchial
37	chr5:112237200-112241800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr5:112237200-112242200	Weak transcription	Brain Angular Gyrus	brain
39	chr5:112237200-112242200	Weak transcription	NH-A	brain
40	chr5:112237200-112249400	Weak transcription	K562	blood
41	chr5:112237400-112242800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:112237400-112254000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr5:112238200-112241800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr5:112238200-112242400	Weak transcription	Left Ventricle	heart
45	chr5:112238200-112242800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr5:112238200-112242800	Weak transcription	Ovary	ovary
47	chr5:112238200-112245200	Weak transcription	Fetal Thymus	thymus
48	chr5:112238200-112249600	Weak transcription	Brain Germinal Matrix	brain
49	chr5:112238200-112251600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr5:112238400-112241600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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