Variant report

Variant	rs10889059
Chromosome Location	chr1:58095791-58095792
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10443241	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789052	0.88[CEU][hapmap]
rs10889061	0.94[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs11207075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207080	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11207088	0.93[CEU][hapmap];0.86[JPT][hapmap]
rs11207090	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11800684	0.94[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11801131	0.94[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11809742	0.94[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap]
rs12120378	0.94[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap]
rs12123728	0.94[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12124076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125360	0.94[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12125452	0.94[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12127845	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12129296	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133913	0.94[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap]
rs1341316	0.84[CHB][hapmap];0.87[CHD][hapmap];0.88[MEX][hapmap]
rs17430851	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2103142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4076379	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs4244010	0.84[CHB][hapmap]
rs4484949	0.94[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs6675237	0.94[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.96[EUR][1000 genomes]
rs6687594	0.82[CHB][hapmap]
rs72676991	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72676993	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72910551	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7339963	0.94[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs7522826	0.90[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7532516	0.94[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes]
rs7554762	0.94[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7554847	0.94[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1012555	chr1:57950355-58103389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv530017	chr1:58002290-58669736	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv871684	chr1:58021206-58096379	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10889059	SSBP3	cis	cerebellum	SCAN
rs10889059	TMEM59	cis	cerebellum	SCAN
rs10889059	C1orf175	cis	parietal	SCAN
rs10889059	TACSTD2	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58090000-58098200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:58090200-58098000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:58090200-58098000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:58091000-58098800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:58091200-58098000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:58091400-58097600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:58092000-58097400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:58092200-58097400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:58092200-58098200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:58092200-58099000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:58092200-58099000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:58095000-58095800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:58095200-58098800	Weak transcription	Fetal Brain Male	brain
14	chr1:58095400-58096400	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr1:58095600-58096000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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