Variant report

Variant	rs13354540
Chromosome Location	chr5:112197654-112197655
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:112195942-112197882	GM12891	blood:	n/a	n/a
2	POLR2A	chr5:112195946-112198491	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr5:112196575-112198782	HepG2	liver:	n/a	n/a
4	GABPA	chr5:112196370-112197683	A549	lung:	n/a	n/a
5	POLR2A	chr5:112196597-112198045	IMR90	lung:	n/a	n/a
6	EP300	chr5:112197571-112197666	GM12878	blood:	n/a	n/a
7	ARID3A	chr5:112197612-112198098	HepG2	liver:	n/a	n/a
8	MXI1	chr5:112196339-112198542	SK-N-SH	brain:	n/a	n/a
9	SIN3A	chr5:112196707-112197746	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr5:112196502-112197943	MCF10A-Er-Src	breast:	n/a	n/a
11	NFYA	chr5:112197580-112198169	Hela-S3	cervix:	n/a	n/a
12	CHD1	chr5:112196640-112197838	H1-hESC	embryonic stem cell:	n/a	chr5:112196847-112196856
13	GABPA	chr5:112196400-112197915	MCF-7	breast:	n/a	n/a
14	IRF1	chr5:112196499-112197781	K562	blood:	n/a	chr5:112196575-112196586 chr5:112196574-112196585
15	MXI1	chr5:112196392-112197817	IMR90	lung:	n/a	n/a
16	POLR2A	chr5:112197634-112198482	GM12878	blood:	n/a	n/a
17	POLR2A	chr5:112195959-112198286	GM12878	blood:	n/a	n/a
18	SIN3AK20	chr5:112196442-112197660	MCF-7	breast:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:112196028..112199860-chr5:112256680..112260462,5	MCF-7	breast:
2	chr5:112041853..112044653-chr5:112197378..112199089,2	K562	blood:
3	chr5:112195906..112198557-chr5:112198644..112200582,4	MCF-7	breast:
4	chr5:112195408..112199487-chr5:112199566..112202603,4	K562	blood:
5	chr5:112195538..112198310-chr5:112312375..112313895,2	K562	blood:
6	chr5:112195332..112197808-chr5:112240725..112243513,2	K562	blood:
7	chr5:112196670..112199465-chr5:112228539..112231018,2	K562	blood:
8	chr5:112196983..112197664-chr5:112257709..112258331,2	Hela-S3	cervix:
9	chr5:112196139..112198613-chr5:112233393..112236476,4	K562	blood:
10	chr5:112152202..112156283-chr5:112195630..112198484,4	MCF-7	breast:
11	chr5:112195239..112200315-chr5:112255126..112261929,8	MCF-7	breast:
12	chr5:112197171..112198752-chr5:112310924..112312714,2	MCF-7	breast:
13	chr5:112196522..112198362-chr5:112219263..112221236,2	MCF-7	breast:

No data

Variant related genes	Relation type
SRP19	TF binding region
ENSG00000272869	TF binding region
ENSG00000172795	Chromatin interaction
ENSG00000270067	Chromatin interaction
ENSG00000153037	Chromatin interaction
ENSG00000134982	Chromatin interaction
ENSG00000249947	Chromatin interaction
ENSG00000129625	Chromatin interaction
ENSG00000272389	Chromatin interaction
ENSG00000266499	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10078107	0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs10477484	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11241187	0.87[YRI][hapmap]
rs13360625	0.80[YRI][hapmap]
rs17134945	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2229994	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs28460815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34083474	1.00[EUR][1000 genomes]
rs41296563	1.00[EUR][1000 genomes]
rs61995948	1.00[EUR][1000 genomes]
rs73220036	1.00[EUR][1000 genomes]
rs73220037	0.87[EUR][1000 genomes]
rs7735066	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112196000-112198000	Active TSS	GM12878-XiMat	blood
2	chr5:112196200-112197800	Active TSS	Brain Angular Gyrus	brain
3	chr5:112196200-112197800	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr5:112196200-112197800	Active TSS	Rectal Smooth Muscle	rectum
5	chr5:112196200-112198200	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr5:112196200-112198200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:112196400-112197800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr5:112196400-112197800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:112196400-112197800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:112196400-112197800	Active TSS	Colonic Mucosa	Colon
11	chr5:112196400-112197800	Active TSS	Fetal Brain Female	brain
12	chr5:112196400-112197800	Active TSS	Placenta	Placenta
13	chr5:112196400-112197800	Active TSS	Fetal Stomach	stomach
14	chr5:112196400-112197800	Active TSS	Gastric	stomach
15	chr5:112196400-112197800	Active TSS	Ovary	ovary
16	chr5:112196400-112197800	Active TSS	Psoas Muscle	Psoas
17	chr5:112196400-112198000	Active TSS	H9 Cell Line	embryonic stem cell
18	chr5:112196400-112198000	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr5:112196400-112198000	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr5:112196400-112198000	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr5:112196400-112198000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:112196400-112198000	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr5:112196400-112198000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:112196400-112198000	Active TSS	Aorta	Aorta
25	chr5:112196400-112198000	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr5:112196400-112198000	Active TSS	Esophagus	oesophagus
27	chr5:112196400-112198000	Active TSS	Fetal Kidney	kidney
28	chr5:112196400-112198000	Active TSS	Lung	lung
29	chr5:112196400-112198000	Active TSS	Right Atrium	heart
30	chr5:112196400-112198000	Active TSS	NHDF-Ad	bronchial
31	chr5:112196400-112198200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:112196400-112198200	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr5:112196400-112198200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:112196400-112198200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:112196400-112198200	Active TSS	HSMM	muscle
36	chr5:112196400-112198200	Active TSS	HSMMtube	muscle
37	chr5:112196400-112198400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:112196400-112198400	Active TSS	Pancreas	Pancrea
39	chr5:112196400-112198600	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr5:112196400-112198600	Active TSS	Right Ventricle	heart
41	chr5:112196600-112197800	Active TSS	Colon Smooth Muscle	Colon
42	chr5:112196600-112197800	Active TSS	Fetal Muscle Trunk	muscle
43	chr5:112196600-112197800	Active TSS	Left Ventricle	heart
44	chr5:112196600-112197800	Active TSS	Placenta Amnion	Placenta Amnion
45	chr5:112196600-112197800	Active TSS	Stomach Smooth Muscle	stomach
46	chr5:112196600-112197800	Active TSS	Thymus	Thymus
47	chr5:112196600-112197800	Active TSS	Spleen	Spleen
48	chr5:112196600-112198000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:112196600-112198000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr5:112196600-112198000	Active TSS	Fetal Intestine Large	intestine

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