Variant report

Variant	rs1435259
Chromosome Location	chr9:101046441-101046442
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:101045068..101047884-chr9:101049633..101052362,2	MCF-7	breast:
2	chr9:101039245..101044695-chr9:101044948..101050216,8	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10156520	0.81[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10156543	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10818728	0.89[ASN][1000 genomes]
rs10985682	0.90[ASN][1000 genomes]
rs10985714	0.90[ASN][1000 genomes]
rs10985747	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12339418	0.84[ASN][1000 genomes]
rs12341227	0.90[ASN][1000 genomes]
rs12341228	0.88[ASN][1000 genomes]
rs12343605	0.86[ASN][1000 genomes]
rs12347890	0.94[ASN][1000 genomes]
rs12349672	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs12350177	0.90[ASN][1000 genomes]
rs12552446	0.87[ASN][1000 genomes]
rs12553553	0.88[JPT][hapmap]
rs12683370	0.94[ASN][1000 genomes]
rs12685596	0.90[ASN][1000 genomes]
rs12685597	0.90[ASN][1000 genomes]
rs1435255	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1435258	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1435260	0.98[ASN][1000 genomes]
rs16914485	0.90[ASN][1000 genomes]
rs1966664	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4548296	0.92[AFR][1000 genomes]
rs55734037	0.87[ASN][1000 genomes]
rs55740603	0.89[ASN][1000 genomes]
rs56397452	0.85[ASN][1000 genomes]
rs56406831	0.86[ASN][1000 genomes]
rs7037857	0.87[ASN][1000 genomes]
rs73657129	0.86[ASN][1000 genomes]
rs7848351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7848352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7853699	0.93[ASN][1000 genomes]

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	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv831663	chr9:100941048-101109492	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1045780	chr9:100943318-101080389	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv540180	chr9:100943318-101080389	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv831664	chr9:101024862-101205637	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv519818	chr9:101024887-101092316	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1435259	CORO2A	cis	lymphoblastoid	seeQTL
rs1435259	HEMGN	cis	parietal	SCAN
rs1435259	TBC1D2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101037200-101051000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:101039800-101051000	Weak transcription	Fetal Intestine Small	intestine
3	chr9:101041400-101049400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:101043400-101051400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:101043600-101051000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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