Variant report

Variant	rs12503047
Chromosome Location	chr4:80574242-80574243
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10857104	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12512592	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12639849	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17004050	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4290916	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4549410	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55647112	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56190714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56984400	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61114630	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62297626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62297627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62297655	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62297657	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62297658	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7340792	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73830597	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879506	chr4:80316417-80604625	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1002031	chr4:80459528-80759113	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1005152	chr4:80549659-80814456	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12503047	CCNG2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:80571600-80574800	Enhancers	NH-A	brain
2	chr4:80571800-80575400	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr4:80572000-80574800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr4:80572000-80575400	Enhancers	Rectal Smooth Muscle	rectum
5	chr4:80572800-80574800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:80572800-80575400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr4:80572800-80575600	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr4:80572800-80575600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr4:80573000-80575000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:80573000-80575200	Enhancers	Colon Smooth Muscle	Colon
11	chr4:80573200-80574800	Weak transcription	NHEK	skin
12	chr4:80573200-80575000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr4:80573200-80575200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:80573200-80575400	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr4:80573600-80574800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:80573800-80574400	Enhancers	HUVEC	blood vessel
17	chr4:80574000-80574400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:80574000-80574400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr4:80574200-80574600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:80574200-80574600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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