Variant report

Variant	rs1990100
Chromosome Location	chr7:26566970-26566971
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:26565083..26567621-chr7:26568763..26571040,3	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10232686	0.83[EUR][1000 genomes]
rs10232690	0.83[EUR][1000 genomes]
rs10241879	0.83[CEU][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10245341	0.83[CEU][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10262030	0.83[EUR][1000 genomes]
rs10270966	1.00[JPT][hapmap]
rs10277111	0.88[ASN][1000 genomes]
rs10278711	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11768540	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13232269	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1990101	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28687511	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3757655	0.83[CEU][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3757657	0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3801874	0.88[ASN][1000 genomes]
rs6942911	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6943003	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6953147	0.81[EUR][1000 genomes]
rs6976270	0.83[EUR][1000 genomes]
rs6979763	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6980196	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6980328	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs730955	0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs740182	0.85[CHD][hapmap];0.81[ASN][1000 genomes]
rs7779755	0.81[ASN][1000 genomes]
rs979303	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs995992	0.91[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs995993	0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs995994	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029596	chr7:26302739-26737913	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv538804	chr7:26302739-26737913	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
4	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1990100	TRA2A	cis	cerebellum	SCAN
rs1990100	JAZF1	cis	parietal	SCAN
rs1990100	TRA2A	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26566200-26570600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr7:26566200-26570800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr7:26566200-26571000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr7:26566400-26572200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr7:26566800-26567000	Enhancers	Fetal Kidney	kidney

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