Variant report

Variant	rs5007546
Chromosome Location	chr12:20527024-20527025
allele	A/C
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	chr12:20526650-20537070	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:20526429-20529539	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr12:20525145-20531578	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
ENSG00000256879	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10734701	1.00[ASN][1000 genomes]
rs10743369	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10770655	1.00[ASN][1000 genomes]
rs10841515	1.00[ASN][1000 genomes]
rs12370696	1.00[ASN][1000 genomes]
rs1373572	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1373573	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1444631	1.00[ASN][1000 genomes]
rs1444633	1.00[ASN][1000 genomes]
rs1530445	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1822751	1.00[ASN][1000 genomes]
rs1822752	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1822753	1.00[ASN][1000 genomes]
rs1822756	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2417850	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3919734	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4762752	1.00[ASN][1000 genomes]
rs4762951	1.00[ASN][1000 genomes]
rs5014038	1.00[ASN][1000 genomes]
rs7133921	1.00[ASN][1000 genomes]
rs7299430	1.00[ASN][1000 genomes]
rs7964191	1.00[ASN][1000 genomes]
rs7964703	1.00[ASN][1000 genomes]
rs7979838	1.00[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	nsv1048067	chr12:20363755-20874845	Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv541408	chr12:20363755-20874845	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1046870	chr12:20509914-20711535	Active TSS Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	nsv541409	chr12:20509914-20711535	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20520400-20528800	Active TSS	Right Atrium	heart
2	chr12:20520600-20527800	Active TSS	Aorta	Aorta
3	chr12:20520600-20527800	Active TSS	Left Ventricle	heart
4	chr12:20520600-20530400	Active TSS	Right Ventricle	heart
5	chr12:20521000-20527200	Active TSS	Fetal Intestine Large	intestine
6	chr12:20521000-20528000	Active TSS	Stomach Smooth Muscle	stomach
7	chr12:20523400-20529200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:20524000-20527800	Flanking Active TSS	HUVEC	blood vessel
9	chr12:20524400-20528000	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr12:20524600-20530000	Weak transcription	Colonic Mucosa	Colon
11	chr12:20525600-20527400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr12:20525600-20531400	Weak transcription	Osteobl	bone
13	chr12:20525600-20543000	Weak transcription	NHDF-Ad	bronchial
14	chr12:20525800-20527800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr12:20526200-20528000	Enhancers	A549	lung
16	chr12:20526400-20527400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:20526400-20531600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:20526400-20537600	Weak transcription	Fetal Stomach	stomach
19	chr12:20526600-20527400	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr12:20526600-20536800	Enhancers	Colon Smooth Muscle	Colon
21	chr12:20526800-20528400	Active TSS	Hela-S3	cervix
22	chr12:20526800-20528600	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr12:20526800-20530000	Enhancers	Fetal Intestine Small	intestine
24	chr12:20526800-20541000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:20527000-20527400	Weak transcription	Rectal Smooth Muscle	rectum

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