Variant report

Variant	rs2789419
Chromosome Location	chr1:159920826-159920827
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1317520	0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs2249707	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2840582	1.00[CEU][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2840584	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2840585	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806199	0.82[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs59975218	0.90[ASN][1000 genomes]
rs60669636	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[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	nsv872489	chr1:159844819-159940000	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv524006	chr1:159886422-159923111	Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv548055	chr1:159918418-159940000	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159916200-159930600	Weak transcription	Right Atrium	heart
2	chr1:159916800-159923600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:159917000-159923400	Weak transcription	NHEK	skin
4	chr1:159918600-159921400	Enhancers	Placenta Amnion	Placenta Amnion
5	chr1:159919400-159923600	Weak transcription	K562	blood
6	chr1:159919600-159923000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:159919600-159923400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:159919800-159923600	Weak transcription	Esophagus	oesophagus
9	chr1:159919800-159923800	Weak transcription	Fetal Intestine Small	intestine
10	chr1:159919800-159930400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:159920000-159923800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:159920200-159923200	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr1:159920200-159923200	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr1:159920800-159921000	Enhancers	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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