Variant report

Variant	rs4836348
Chromosome Location	chr5:127278773-127278774
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:

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10050374	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10057561	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064559	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10068883	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10213776	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900794	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs11738398	1.00[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs11741283	0.91[EUR][1000 genomes]
rs12517005	0.94[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs13160751	0.98[EUR][1000 genomes]
rs2011576	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2409037	0.94[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs4836344	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4836346	0.98[EUR][1000 genomes]
rs55896045	0.91[EUR][1000 genomes]
rs6595796	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6871743	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877403	0.92[EUR][1000 genomes]
rs6889756	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes]
rs6898956	0.87[EUR][1000 genomes]
rs758181	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7706518	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7717741	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs7726011	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9327463	0.82[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4836348	SLC12A2	cis	cerebellum	SCAN
rs4836348	LOC644869	cis	multi-tissue	Pritchard
rs4836348	CDC42SE2	cis	cerebellum	SCAN

Chromatin state (count:29 , 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	chr5:127276600-127279200	Enhancers	Small Intestine	intestine
8	chr5:127276600-127281800	Enhancers	A549	lung
9	chr5:127277000-127279400	Enhancers	Stomach Mucosa	stomach
10	chr5:127277200-127280000	Enhancers	HUVEC	blood vessel
11	chr5:127277600-127279400	Weak transcription	Gastric	stomach
12	chr5:127277800-127278800	Enhancers	GM12878-XiMat	blood
13	chr5:127277800-127278800	Enhancers	Hela-S3	cervix
14	chr5:127278000-127278800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:127278000-127279800	Enhancers	Duodenum Mucosa	Duodenum
16	chr5:127278200-127279200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:127278400-127279000	Enhancers	Muscle Satellite Cultured Cells	--
18	chr5:127278400-127281800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr5:127278400-127283000	Weak transcription	HMEC	breast
20	chr5:127278400-127286400	Weak transcription	Fetal Intestine Large	intestine
21	chr5:127278400-127286400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr5:127278400-127292800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr5:127278400-127292800	Weak transcription	Brain Substantia Nigra	brain
24	chr5:127278400-127292800	Weak transcription	HSMM	muscle
25	chr5:127278400-127294600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr5:127278400-127295600	Weak transcription	HSMMtube	muscle
27	chr5:127278600-127279000	Weak transcription	Fetal Intestine Small	intestine
28	chr5:127278600-127279200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:127278600-127279800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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