Variant report

Variant	rs12030141
Chromosome Location	chr1:224676328-224676329
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10916626	0.82[EUR][1000 genomes]
rs1341868	0.84[AFR][1000 genomes]
rs1891243	0.83[EUR][1000 genomes]
rs2405027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35143345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4654041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6688925	0.86[EUR][1000 genomes]
rs7532359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7539200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7543628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][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	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12030141	CNIH4	cis	Muscle Skeletal	GTEx
rs12030141	CNIH4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224671000-224676400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:224674800-224677800	Enhancers	H9 Cell Line	embryonic stem cell
3	chr1:224675200-224676800	Weak transcription	GM12878-XiMat	blood
4	chr1:224675200-224677000	Weak transcription	HSMMtube	muscle
5	chr1:224675200-224677200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:224675400-224677000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:224676200-224677200	Enhancers	NHLF	lung
8	chr1:224676200-224677600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
9	chr1:224676200-224677600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:224676200-224677600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:224676200-224677600	Enhancers	HMEC	breast
12	chr1:224676200-224677800	Enhancers	NHEK	skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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