Variant report

Variant	rs9890857
Chromosome Location	chr17:53567193-53567194
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11079175	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2009355	0.80[EUR][1000 genomes]
rs4423478	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4476231	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6504964	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6504966	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7208128	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7212345	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7214882	0.94[CEU][hapmap];0.95[CHB][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7216168	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7216551	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7225620	0.87[EUR][1000 genomes]
rs7225654	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7226365	0.87[EUR][1000 genomes]
rs8068248	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8069317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9303369	0.82[TSI][hapmap]
rs9891477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv2100	chr17:53492380-54328516	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1062337	chr17:53510996-54161442	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv833490	chr17:53564973-53612482	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:53565200-53570200	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr17:53565400-53573600	Weak transcription	Colon Smooth Muscle	Colon
3	chr17:53565600-53570000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr17:53565600-53570000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr17:53565600-53570000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr17:53565600-53570000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr17:53565600-53570200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:53565600-53570200	Weak transcription	Fetal Lung	lung
9	chr17:53565600-53570400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr17:53565800-53570000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr17:53565800-53573600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr17:53566000-53570200	Weak transcription	A549	lung
13	chr17:53566200-53569800	Weak transcription	HepG2	liver
14	chr17:53566400-53569600	Enhancers	Fetal Brain Male	brain
15	chr17:53566400-53570200	Weak transcription	Adipose Nuclei	Adipose
16	chr17:53566600-53573000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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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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