Variant report

Variant	rs12523578
Chromosome Location	chr5:80601208-80601209
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	chr5:80600807-80601219	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr5:80600829-80602142	K562	blood:	n/a	n/a

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

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

Extended variants
information (count: 27 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10514218	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942946	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11739833	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739834	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743842	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743849	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745275	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11749113	1.00[CEU][hapmap]
rs11953113	0.94[EUR][1000 genomes]
rs11957137	0.94[EUR][1000 genomes]
rs12516089	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12517538	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12518716	0.96[EUR][1000 genomes]
rs16878594	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16878597	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17231292	1.00[ASN][1000 genomes]
rs62365025	0.81[EUR][1000 genomes]
rs62365032	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62365035	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62365038	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62365866	0.82[EUR][1000 genomes]
rs72771170	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72771190	1.00[ASN][1000 genomes]
rs72771198	1.00[ASN][1000 genomes]
rs72773017	1.00[ASN][1000 genomes]
rs7731320	0.83[AMR][1000 genomes];0.96[EUR][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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12523578	CTC-281B15.1	cis	Artery Tibial	GTEx
rs12523578	CTC-281B15.1	cis	Skin Sun Exposed Lower leg	GTEx
rs12523578	CTC-281B15.1	cis	Thyroid	GTEx
rs12523578	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs12523578	CTC-281B15.1	cis	Nerve Tibial	GTEx
rs12523578	CTC-281B15.1	cis	Adipose Subcutaneous	GTEx
rs12523578	CTC-281B15.1	cis	lung	GTEx
rs12523578	CTC-281B15.1	cis	Esophagus Mucosa	GTEx
rs12523578	CTC-281B15.1	cis	Artery Aorta	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	chr5:80598400-80604800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr5:80598400-80605200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr5:80598400-80606800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:80598400-80606800	Weak transcription	Right Ventricle	heart
7	chr5:80598400-80611200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:80598600-80604400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr5:80598600-80604400	Weak transcription	Psoas Muscle	Psoas
10	chr5:80598600-80604800	Weak transcription	Primary B cells from cord blood	blood
11	chr5:80598600-80605000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr5:80598600-80605000	Weak transcription	Placenta	Placenta
13	chr5:80598600-80605000	Weak transcription	Left Ventricle	heart
14	chr5:80598600-80605000	Weak transcription	HUVEC	blood vessel
15	chr5:80598600-80605200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr5:80598600-80605400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr5:80598600-80606400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:80598600-80606400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:80598600-80606400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:80598600-80606400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr5:80598600-80606600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:80598600-80606600	Weak transcription	Aorta	Aorta
23	chr5:80598600-80606600	Weak transcription	Brain Hippocampus Middle	brain
24	chr5:80598600-80606600	Weak transcription	Fetal Intestine Small	intestine
25	chr5:80598600-80606600	Weak transcription	Lung	lung
26	chr5:80598600-80606600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr5:80598600-80606600	Weak transcription	HSMMtube	muscle
28	chr5:80598600-80606800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr5:80598600-80607000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr5:80598600-80607600	Weak transcription	Fetal Kidney	kidney
31	chr5:80598600-80608200	Weak transcription	Fetal Stomach	stomach
32	chr5:80598600-80608800	Weak transcription	Brain Germinal Matrix	brain
33	chr5:80598600-80609600	Weak transcription	Gastric	stomach
34	chr5:80598600-80610000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr5:80598600-80611200	Weak transcription	Brain Anterior Caudate	brain
36	chr5:80598600-80611200	Weak transcription	Fetal Brain Male	brain
37	chr5:80598600-80611200	Weak transcription	Small Intestine	intestine
38	chr5:80598600-80611200	Weak transcription	Stomach Mucosa	stomach
39	chr5:80598600-80611800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr5:80598800-80604000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:80598800-80605000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr5:80598800-80606600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr5:80598800-80606800	Weak transcription	Fetal Brain Female	brain
44	chr5:80598800-80611000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr5:80598800-80611200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:80599200-80604400	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr5:80599200-80610000	Weak transcription	Pancreas	Pancrea
48	chr5:80599200-80612200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr5:80599400-80604800	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr5:80599400-80610400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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