Variant report

Variant	rs2240404
Chromosome Location	chr7:30707302-30707303
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:30706585..30709994-chr7:30711601..30714014,3	K562	blood:
2	chr7:30706056..30708337-chr7:30709975..30712039,2	K562	blood:
3	chr7:30701796..30704205-chr7:30705913..30708503,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs2072236	1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs2074779	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2240400	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs2240403	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs2267716	0.81[JPT][hapmap]
rs2270008	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284216	0.81[JPT][hapmap]
rs2527878	0.89[ASN][1000 genomes]
rs2527879	0.90[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs2527880	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2529438	0.89[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs2529439	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs2529442	0.99[ASN][1000 genomes]
rs2709806	0.99[ASN][1000 genomes]
rs38439	0.84[CHD][hapmap]
rs38476	1.00[JPT][hapmap]
rs38491	0.95[ASN][1000 genomes]
rs38492	0.95[ASN][1000 genomes]
rs38496	0.95[ASN][1000 genomes]
rs39739	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs41320047	0.99[ASN][1000 genomes]
rs4526262	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs4723000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723002	0.81[JPT][hapmap]
rs4723003	0.81[JPT][hapmap]
rs6945035	0.95[ASN][1000 genomes]
rs6949955	0.99[ASN][1000 genomes]
rs728539	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs73294450	0.99[ASN][1000 genomes]
rs758000	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs7791663	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv538811	chr7:30549595-31405593	Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1016256	chr7:30649212-31163056	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1023120	chr7:30655070-31185096	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv2761316	chr7:30655082-31166676	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv527038	chr7:30657467-31161945	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv916877	chr7:30661135-31154731	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1017168	chr7:30663213-31166676	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv1017808	chr7:30671936-31150473	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv830938	chr7:30684230-30897523	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2240404	HOXA11	cis	cerebellum	SCAN
rs2240404	LOC441208	cis	cerebellum	SCAN
rs2240404	CYP1B1	trans	brain	seeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30696200-30707600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:30701000-30707800	Weak transcription	Fetal Brain Female	brain
3	chr7:30704800-30712000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:30705400-30711800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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