Variant report

Variant	rs17115739
Chromosome Location	chr1:57863387-57863388
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10159302	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs10493218	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11207023	1.00[JPT][hapmap]
rs11800574	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11803541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11805025	1.00[JPT][hapmap]
rs11807631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1424471	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs17096836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17115683	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17115713	1.00[JPT][hapmap]
rs17115722	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17115757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17115765	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17115767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs17115834	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17115844	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1778031	0.92[EUR][1000 genomes]
rs17838097	0.80[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1981891	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2805873	1.00[CHB][hapmap]
rs35664891	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3738552	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3850553	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3850554	1.00[ASW][hapmap];0.80[CEU][hapmap];0.94[GIH][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4912242	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4912243	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4912245	0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs507466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs524941	0.89[EUR][1000 genomes]
rs566739	1.00[JPT][hapmap]
rs60790797	0.92[EUR][1000 genomes]
rs6657926	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs72909225	0.92[EUR][1000 genomes]
rs72909227	0.92[EUR][1000 genomes]
rs72909233	0.92[EUR][1000 genomes]
rs72909245	0.92[EUR][1000 genomes]
rs7541150	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7541309	0.88[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	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv954	chr1:57823140-57865799	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1001771	chr1:57837089-58068175	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57858000-57868600	Weak transcription	Fetal Brain Male	brain
2	chr1:57860200-57865400	Weak transcription	HepG2	liver
3	chr1:57860200-57865600	Weak transcription	Fetal Intestine Small	intestine
4	chr1:57860400-57863400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:57860400-57863800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:57860400-57874600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:57860600-57863400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:57862400-57870800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:57862400-57873200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:57863200-57864000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:57863200-57864000	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr1:57863200-57864200	Enhancers	HUES64 Cell Line	embryonic stem cell

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