Variant report

Variant	rs7527779
Chromosome Location	chr1:196308262-196308263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10922051	1.00[JPT][hapmap]
rs10922057	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11801881	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs11806479	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12058062	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs12127589	1.00[JPT][hapmap]
rs12402127	0.90[AFR][1000 genomes]
rs12407399	0.82[GIH][hapmap]
rs12410633	0.82[GIH][hapmap]
rs1339951	1.00[CHD][hapmap]
rs16839682	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16839685	0.85[ASN][1000 genomes]
rs16839693	0.85[ASN][1000 genomes]
rs16839700	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16839771	1.00[ASN][1000 genomes]
rs16839782	1.00[ASN][1000 genomes]
rs16839785	0.82[GIH][hapmap]
rs16839791	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16839822	1.00[ASN][1000 genomes]
rs16839841	1.00[CHD][hapmap]
rs16839886	1.00[CHD][hapmap]
rs16839905	1.00[CHD][hapmap]
rs16839906	1.00[CHD][hapmap]
rs1924755	1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes]
rs1924757	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1924759	1.00[JPT][hapmap]
rs1925332	1.00[JPT][hapmap]
rs2025599	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs2245414	1.00[JPT][hapmap]
rs2296269	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2477354	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs2477356	1.00[JPT][hapmap]
rs2477357	1.00[JPT][hapmap]
rs2477359	1.00[JPT][hapmap]
rs2477361	1.00[JPT][hapmap]
rs2477554	1.00[JPT][hapmap]
rs41451950	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4379659	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs533228	1.00[JPT][hapmap]
rs564157	1.00[JPT][hapmap]
rs61328263	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61710289	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73065825	0.90[AFR][1000 genomes]
rs73065828	0.90[AFR][1000 genomes]
rs73065831	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73065837	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74133631	0.85[ASN][1000 genomes]
rs74136510	0.90[AFR][1000 genomes]
rs7537176	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs7544651	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs7547827	1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs7552975	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs7554401	0.87[AFR][1000 genomes]
rs912760	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs9725530	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9970935	1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	esv1826904	chr1:196291977-196371432	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
7	nsv1009233	chr1:196301712-196568874	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
8	nsv872954	chr1:196304863-196387809	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196266200-196309600	Weak transcription	Fetal Kidney	kidney
2	chr1:196273000-196313400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:196275800-196313000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:196279400-196314400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:196298000-196313400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:196298800-196311200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:196300200-196313600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:196301800-196313400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:196303200-196311000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:196303200-196311600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:196303200-196312000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:196303200-196332600	Weak transcription	Ovary	ovary
13	chr1:196305400-196309200	Strong transcription	Liver	Liver
14	chr1:196306800-196314200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:196307600-196309200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:196307600-196310400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:196308200-196308800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:196308200-196309200	Strong transcription	HUES6 Cell Line	embryonic stem cell

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