Variant report

Variant	rs2409037
Chromosome Location	chr5:127286190-127286191
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:127277558..127280504-chr5:127284897..127288204,4	MCF-7	breast:
2	chr5:127283928..127287234-chr5:127417993..127420755,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245937	Chromatin interaction
ENSG00000064651	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10037914	0.87[ASN][1000 genomes]
rs10041355	0.80[ASN][1000 genomes]
rs10041388	0.80[ASN][1000 genomes]
rs10050374	0.92[EUR][1000 genomes]
rs10057561	0.86[EUR][1000 genomes]
rs10065448	0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs10072806	0.83[JPT][hapmap]
rs10074995	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10079317	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10463834	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs10478786	0.80[ASN][1000 genomes]
rs10478787	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs10900794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738398	0.94[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs11740438	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11740439	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11741283	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12517005	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12523625	0.81[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap]
rs12653621	0.85[ASN][1000 genomes]
rs12658023	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13160751	0.90[EUR][1000 genomes]
rs13174053	0.80[ASN][1000 genomes]
rs13180050	0.80[ASN][1000 genomes]
rs13361741	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1520246	1.00[JPT][hapmap]
rs2011576	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs2108654	0.80[ASN][1000 genomes]
rs2409038	0.80[ASN][1000 genomes]
rs2409039	0.80[ASN][1000 genomes]
rs28473744	0.92[ASN][1000 genomes]
rs28542972	0.92[ASN][1000 genomes]
rs28567046	0.92[ASN][1000 genomes]
rs28591675	0.94[ASN][1000 genomes]
rs28636438	0.92[ASN][1000 genomes]
rs28687461	0.92[ASN][1000 genomes]
rs28736542	0.92[ASN][1000 genomes]
rs28816429	0.92[ASN][1000 genomes]
rs2898077	0.80[ASN][1000 genomes]
rs4835934	0.80[ASN][1000 genomes]
rs4836344	0.83[EUR][1000 genomes]
rs4836345	1.00[JPT][hapmap]
rs4836346	0.90[EUR][1000 genomes]
rs4836348	0.92[EUR][1000 genomes]
rs55896045	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59634534	0.80[ASN][1000 genomes]
rs6595796	0.82[CEU][hapmap]
rs6871743	0.86[EUR][1000 genomes]
rs6877403	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881456	0.80[ASN][1000 genomes]
rs6889756	0.94[CEU][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs6892704	0.81[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs6898956	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732235	0.80[ASN][1000 genomes]
rs732236	0.81[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs758181	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs7706518	0.92[EUR][1000 genomes]
rs7717741	0.94[CEU][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs9327457	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2409037	CDC42SE2	cis	cerebellum	SCAN
rs2409037	SLC12A2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127267400-127292200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:127269800-127292400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:127271200-127294800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:127274400-127287000	Weak transcription	Primary T cells from cord blood	blood
5	chr5:127274800-127295000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:127274800-127296000	Weak transcription	Primary B cells from cord blood	blood
7	chr5:127278400-127286400	Weak transcription	Fetal Intestine Large	intestine
8	chr5:127278400-127286400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr5:127278400-127292800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr5:127278400-127292800	Weak transcription	Brain Substantia Nigra	brain
11	chr5:127278400-127292800	Weak transcription	HSMM	muscle
12	chr5:127278400-127294600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr5:127278400-127295600	Weak transcription	HSMMtube	muscle
14	chr5:127280200-127292800	Weak transcription	Gastric	stomach
15	chr5:127281600-127286400	Weak transcription	Fetal Intestine Small	intestine
16	chr5:127281800-127295400	Weak transcription	Psoas Muscle	Psoas
17	chr5:127285000-127286600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr5:127285200-127295200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr5:127285800-127286400	Enhancers	A549	lung
20	chr5:127285800-127303800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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