Variant report

Variant	rs17541479
Chromosome Location	chr1:57640721-57640722
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10789044	0.91[AMR][1000 genomes]
rs10789045	0.91[AMR][1000 genomes]
rs10889026	0.84[TSI][hapmap];0.91[AMR][1000 genomes]
rs12034636	0.91[AMR][1000 genomes]
rs12073675	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs12120310	0.91[AMR][1000 genomes]
rs12123599	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1413226	0.89[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1504588	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1504589	0.89[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17482565	0.82[CEU][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17541356	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4912429	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4912430	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4912431	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4912432	0.89[ASW][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs55944821	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs6670988	0.82[CEU][hapmap];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6680219	0.89[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs7548633	0.84[TSI][hapmap];0.87[AMR][1000 genomes]
rs7552759	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57624000-57644800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:57636600-57641400	Weak transcription	Fetal Intestine Small	intestine
3	chr1:57637600-57641400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:57637800-57640800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:57638600-57644800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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