Variant report

Variant	rs11589238
Chromosome Location	chr1:97747164-97747165
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10157665	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10465749	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11583545	0.80[EUR][1000 genomes]
rs12029106	1.00[CEU][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12030332	0.91[EUR][1000 genomes]
rs12046744	1.00[CEU][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12049622	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2049112	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28755414	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4264037	1.00[CEU][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56300389	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57555420	0.81[EUR][1000 genomes]
rs58203161	0.81[EUR][1000 genomes]
rs61786278	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61786354	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61787967	0.82[EUR][1000 genomes]
rs6700670	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72726670	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72726689	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7527272	0.95[CEU][hapmap];0.89[TSI][hapmap];0.88[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	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	nsv546864	chr1:97744048-97764073	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
7	nsv871536	chr1:97744048-97771947	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11589238	SASS6	cis	cerebellum	SCAN
rs11589238	MTF2	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97720600-97772000	Weak transcription	Ovary	ovary
2	chr1:97724000-97773200	Weak transcription	Lung	lung
3	chr1:97730400-97769800	Weak transcription	Primary B cells from cord blood	blood
4	chr1:97731400-97761200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr1:97731600-97757600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:97731600-97757800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:97733400-97748800	Weak transcription	Dnd41	blood
8	chr1:97733600-97769800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:97736800-97747600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:97736800-97771600	Weak transcription	Left Ventricle	heart
11	chr1:97737800-97750400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:97737800-97771600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:97738800-97766200	Weak transcription	Adipose Nuclei	Adipose
14	chr1:97743000-97750600	Weak transcription	Liver	Liver
15	chr1:97743000-97759600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:97743800-97769800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr1:97744000-97750400	Weak transcription	HSMM	muscle
18	chr1:97744000-97758000	Weak transcription	Primary T cells from cord blood	blood
19	chr1:97744200-97752200	Weak transcription	HSMMtube	muscle
20	chr1:97745000-97773400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:97745200-97748200	Weak transcription	Hela-S3	cervix
22	chr1:97745200-97771800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:97745200-97773400	Weak transcription	NHDF-Ad	bronchial
24	chr1:97745800-97769800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:97746000-97770600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:97746200-97752800	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr1:97746400-97750400	Weak transcription	Monocytes-CD14+_RO01746	blood

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