Variant report

Variant	rs7522938
Chromosome Location	chr1:97727820-97727821
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:97727419..97728945-chr1:97737603..97739264,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10783057	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783058	0.80[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875061	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875062	0.80[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10875064	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11165826	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11165827	0.94[CEU][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11165829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11165837	0.90[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12024830	0.85[CEU][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1402258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1589342	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1589343	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1610253	0.86[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2090763	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28483122	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28595744	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4285754	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4950026	0.85[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs641805	0.81[JPT][hapmap]
rs6689930	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6700920	0.85[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7512040	0.96[LWK][hapmap];0.85[MKK][hapmap];0.87[YRI][hapmap]
rs7539889	0.81[GIH][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491816	chr1:97266403-98223619	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv530048	chr1:97457175-98031501	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007950	chr1:97466488-98021146	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv533039	chr1:97665736-98343102	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv470728	chr1:97703325-97761972	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv947498	chr1:97726115-97730467	Weak transcription Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97699600-97729000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:97700600-97733000	Weak transcription	Dnd41	blood
3	chr1:97716800-97733000	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr1:97718400-97736600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:97719200-97733800	Weak transcription	Liver	Liver
6	chr1:97719600-97733000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:97720600-97736600	Weak transcription	Adipose Nuclei	Adipose
8	chr1:97720600-97772000	Weak transcription	Ovary	ovary
9	chr1:97724000-97736600	Weak transcription	Small Intestine	intestine
10	chr1:97724000-97773200	Weak transcription	Lung	lung
11	chr1:97724400-97740200	Weak transcription	Primary T cells from cord blood	blood
12	chr1:97726600-97733000	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr1:97727200-97728400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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