Variant report

Variant	rs2457832
Chromosome Location	chr1:62635116-62635117
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs2251367	0.82[EUR][1000 genomes]
rs2264960	0.84[EUR][1000 genomes]
rs2476196	0.82[EUR][1000 genomes]
rs2476197	0.86[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs2481669	0.82[EUR][1000 genomes]
rs2481672	0.86[CEU][hapmap];0.91[GIH][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs2481674	0.90[CEU][hapmap];0.81[CHB][hapmap];0.80[TSI][hapmap];0.90[EUR][1000 genomes]
rs2481680	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481706	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666468	0.83[EUR][1000 genomes]
rs2666491	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs2666493	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs2774932	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs2984823	0.82[EUR][1000 genomes]
rs2989012	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587956	0.83[EUR][1000 genomes]
rs7530787	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7535875	0.80[EUR][1000 genomes]
rs7538266	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv461650	chr1:62542717-62657530	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv546417	chr1:62542717-62657530	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1012683	chr1:62587852-62643998	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2457832	ATG4C	cis	cerebellum	SCAN
rs2457832	MYSM1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62593600-62636200	Weak transcription	Spleen	Spleen
2	chr1:62608400-62643600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:62613400-62636000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:62618600-62637800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:62621200-62636600	Weak transcription	Fetal Intestine Large	intestine
6	chr1:62622600-62638000	Weak transcription	Fetal Intestine Small	intestine
7	chr1:62627000-62642400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:62634400-62636000	Enhancers	HepG2	liver
9	chr1:62634600-62640600	Weak transcription	Fetal Lung	lung

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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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