Variant report

Variant	rs12405952
Chromosome Location	chr1:70602492-70602493
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11581894	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17463887	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs269273	0.87[ASN][1000 genomes]
rs269275	0.93[ASN][1000 genomes]
rs269277	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs269282	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4650029	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678418	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531879	chr1:70386455-70644617	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1005397	chr1:70598803-70634585	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12405952	CTH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70596800-70609200	Weak transcription	Liver	Liver
2	chr1:70599000-70606000	Weak transcription	Osteobl	bone
3	chr1:70599000-70606600	Weak transcription	K562	blood
4	chr1:70599000-70609600	Weak transcription	GM12878-XiMat	blood
5	chr1:70600200-70602800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:70600200-70605600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:70600200-70606000	Weak transcription	Aorta	Aorta
8	chr1:70600400-70602600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:70600400-70604600	Weak transcription	Fetal Brain Female	brain
10	chr1:70600400-70605200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:70600400-70605600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:70600400-70605800	Weak transcription	NHDF-Ad	bronchial
13	chr1:70600600-70602800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:70600600-70605200	Weak transcription	Brain Germinal Matrix	brain
15	chr1:70600600-70605200	Weak transcription	Fetal Heart	heart
16	chr1:70601000-70615400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:70601000-70643200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:70601200-70605400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:70601200-70606000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:70601200-70606200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:70601200-70652000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:70601800-70605200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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