Variant report

Variant	rs11807554
Chromosome Location	chr1:221838876-221838877
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10449304	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11803842	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12118810	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12132407	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12134883	0.83[ASW][hapmap];1.00[CHB][hapmap]
rs12136282	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12136283	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12136513	0.82[ASN][1000 genomes]
rs12728570	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12758057	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2095730	1.00[CHB][hapmap]
rs2176690	0.82[ASN][1000 genomes]
rs6685165	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66864883	0.98[ASN][1000 genomes]
rs67079790	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs68170611	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7532154	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540426	0.89[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	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv873200	chr1:221644180-221843191	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11807554	BPNT1	cis	parietal	SCAN
rs11807554	SLC30A10	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221837200-221839200	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr1:221837400-221840400	Weak transcription	HMEC	breast
3	chr1:221837400-221840600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:221837400-221840600	Weak transcription	Stomach Mucosa	stomach
5	chr1:221837400-221840600	Weak transcription	Hela-S3	cervix
6	chr1:221837600-221839000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr1:221837800-221839000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr1:221837800-221839000	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr1:221838000-221840600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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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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