Variant report

Variant	rs11738398
Chromosome Location	chr5:127272483-127272484
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	chr5:127267226..127272789-chr5:127416073..127421756,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000064651	Chromatin interaction
ENSG00000245937	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10050374	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10057561	0.94[EUR][1000 genomes]
rs10064559	0.83[EUR][1000 genomes]
rs10068883	0.83[EUR][1000 genomes]
rs10900794	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs11741283	0.87[EUR][1000 genomes]
rs12517005	0.94[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs13160751	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409037	0.94[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs4836344	0.91[EUR][1000 genomes]
rs4836346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4836348	0.96[EUR][1000 genomes]
rs55896045	0.87[EUR][1000 genomes]
rs6595796	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs6871743	0.91[EUR][1000 genomes]
rs6877403	0.88[EUR][1000 genomes]
rs6889756	1.00[CEU][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs6898956	0.83[EUR][1000 genomes]
rs758181	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7706518	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7717741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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
rs11738398	SLC12A2	cis	cerebellum	SCAN
rs11738398	CDC42SE2	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127266600-127277000	Weak transcription	Aorta	Aorta
2	chr5:127267400-127292200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr5:127269800-127292400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:127270200-127272600	Enhancers	NHEK	skin
5	chr5:127270400-127272600	Enhancers	Stomach Mucosa	stomach
6	chr5:127270800-127273400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:127271200-127274400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:127271200-127276800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr5:127271200-127294800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:127271400-127273000	Enhancers	A549	lung
11	chr5:127271400-127276600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:127271400-127276800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:127271400-127277000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:127271600-127276800	Weak transcription	Fetal Intestine Small	intestine
15	chr5:127271600-127276800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr5:127271600-127277000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:127271800-127272800	Enhancers	GM12878-XiMat	blood
18	chr5:127272000-127272600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr5:127272000-127272600	Enhancers	Small Intestine	intestine
20	chr5:127272000-127272600	Enhancers	Thymus	Thymus
21	chr5:127272200-127272600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
22	chr5:127272400-127272600	Enhancers	Lung	lung
23	chr5:127272400-127272600	Enhancers	Pancreas	Pancrea
24	chr5:127272400-127277400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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