Variant report

Variant	rs12517538
Chromosome Location	chr5:80600006-80600007
allele	A/G
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	chr5:80599884-80600055	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr5:80599305-80600190	MCF10A-Er-Src	breast:	n/a	n/a
3	RCOR1	chr5:80599177-80600177	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:80599729..80604075-chr5:80605851..80609625,4	K562	blood:
2	chr5:80599288..80602129-chr5:80607036..80608849,2	K562	blood:
3	chr5:80598755..80600911-chr5:80604785..80606382,2	K562	blood:

Variant related genes	Relation type
CKMT2-AS1	TF binding region
ZCCHC9	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10514218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10942946	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739833	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11739834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11740916	1.00[ASN][1000 genomes]
rs11743842	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11743849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11745275	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749113	0.93[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11953113	0.97[EUR][1000 genomes]
rs11957137	0.97[EUR][1000 genomes]
rs12516089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12518716	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12523578	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16878594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16878597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56067803	1.00[ASN][1000 genomes]
rs62365025	0.84[EUR][1000 genomes]
rs62365031	1.00[ASN][1000 genomes]
rs62365032	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62365035	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62365038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62365866	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62365867	1.00[ASN][1000 genomes]
rs72771170	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7731320	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12517538	CTC-281B15.1	cis	Artery Tibial	GTEx
rs12517538	CTC-281B15.1	cis	Nerve Tibial	GTEx
rs12517538	CTC-281B15.1	cis	Stomach	GTEx
rs12517538	CTC-281B15.1	cis	Thyroid	GTEx
rs12517538	CTC-281B15.1	cis	Adipose Subcutaneous	GTEx
rs12517538	CTC-281B15.1	cis	Esophagus Mucosa	GTEx
rs12517538	CTC-281B15.1	cis	Skin Sun Exposed Lower leg	GTEx
rs12517538	CTC-281B15.1	cis	lung	GTEx
rs12517538	CTC-281B15.1	cis	Artery Aorta	GTEx
rs12517538	CTC-281B15.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80598000-80605200	Weak transcription	Ovary	ovary
2	chr5:80598200-80612400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:80598400-80600600	Weak transcription	Colonic Mucosa	Colon
4	chr5:80598400-80600600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr5:80598400-80600600	Weak transcription	Thymus	Thymus
6	chr5:80598400-80601200	Weak transcription	Esophagus	oesophagus
7	chr5:80598400-80604800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr5:80598400-80605200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr5:80598400-80606800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr5:80598400-80606800	Weak transcription	Right Ventricle	heart
11	chr5:80598400-80611200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:80598600-80600200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr5:80598600-80600200	Enhancers	Liver	Liver
14	chr5:80598600-80600200	Enhancers	HMEC	breast
15	chr5:80598600-80600200	Enhancers	Osteobl	bone
16	chr5:80598600-80600400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:80598600-80600600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:80598600-80600600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr5:80598600-80600600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr5:80598600-80600600	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr5:80598600-80600600	Weak transcription	Fetal Muscle Leg	muscle
22	chr5:80598600-80600600	Weak transcription	Fetal Thymus	thymus
23	chr5:80598600-80600600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr5:80598600-80600600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr5:80598600-80600600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr5:80598600-80600800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr5:80598600-80600800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr5:80598600-80600800	Weak transcription	Colon Smooth Muscle	Colon
29	chr5:80598600-80600800	Weak transcription	Fetal Intestine Large	intestine
30	chr5:80598600-80601200	Weak transcription	Spleen	Spleen
31	chr5:80598600-80604400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr5:80598600-80604400	Weak transcription	Psoas Muscle	Psoas
33	chr5:80598600-80604800	Weak transcription	Primary B cells from cord blood	blood
34	chr5:80598600-80605000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr5:80598600-80605000	Weak transcription	Placenta	Placenta
36	chr5:80598600-80605000	Weak transcription	Left Ventricle	heart
37	chr5:80598600-80605000	Weak transcription	HUVEC	blood vessel
38	chr5:80598600-80605200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr5:80598600-80605400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr5:80598600-80606400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr5:80598600-80606400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:80598600-80606400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr5:80598600-80606400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr5:80598600-80606600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr5:80598600-80606600	Weak transcription	Aorta	Aorta
46	chr5:80598600-80606600	Weak transcription	Brain Hippocampus Middle	brain
47	chr5:80598600-80606600	Weak transcription	Fetal Intestine Small	intestine
48	chr5:80598600-80606600	Weak transcription	Lung	lung
49	chr5:80598600-80606600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr5:80598600-80606600	Weak transcription	HSMMtube	muscle

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