Variant report

Variant	rs16839785
Chromosome Location	chr1:196291365-196291366
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10494742	1.00[ASW][hapmap];0.89[CEU][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11806479	0.82[GIH][hapmap]
rs12402127	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12405050	0.88[EUR][1000 genomes]
rs12407399	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12409953	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12410633	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56186308	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56199993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60040626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73063982	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73063989	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73063993	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73065807	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73065818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73065825	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73065828	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73065844	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73067629	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs74136510	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7513135	0.89[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7522690	0.89[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7527779	0.82[GIH][hapmap]
rs7529369	0.90[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs7537176	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7554401	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872952	chr1:196174790-196304223	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv548741	chr1:196186750-196293493	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv832237	chr1:196205674-196328500	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv469680	chr1:196259846-196419016	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv482746	chr1:196259846-196419016	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv931415	chr1:196270759-196744780	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv872953	chr1:196286639-196411281	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16839785	SYCE1	trans	lymphoblastoid	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196256600-196302800	Weak transcription	Ovary	ovary
2	chr1:196266200-196309600	Weak transcription	Fetal Kidney	kidney
3	chr1:196268800-196304400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr1:196273000-196313400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:196275800-196313000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:196276000-196305000	Weak transcription	Fetal Lung	lung
7	chr1:196279400-196314400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:196282600-196298600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:196285200-196295200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:196285200-196295800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:196285200-196296000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:196285200-196299800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:196285200-196302200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:196285200-196303800	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:196287000-196296400	Weak transcription	Liver	Liver
16	chr1:196290400-196293000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:196290800-196293200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:196291000-196292800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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