Variant report

Variant	rs11739301
Chromosome Location	chr5:74172468-74172469
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	chr5:74161003..74163055-chr5:74170808..74173347,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198780	Chromatin interaction
ENSG00000271714	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10515189	0.83[JPT][hapmap]
rs11738903	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11740809	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743655	0.83[JPT][hapmap]
rs11746069	0.83[JPT][hapmap]
rs11746561	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap]
rs11746611	0.83[JPT][hapmap]
rs58010984	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60270014	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62367768	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62367770	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62367771	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62367773	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62367774	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62367819	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62367823	0.87[ASN][1000 genomes]
rs62367824	0.87[ASN][1000 genomes]
rs62367825	0.87[ASN][1000 genomes]
rs62367828	0.86[ASN][1000 genomes]
rs820828	0.83[JPT][hapmap]
rs820830	0.83[JPT][hapmap]
rs820834	0.83[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518286	chr5:74169045-74243120	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS 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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11739301	NSA2	cis	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74169400-74173000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:74171800-74172600	Flanking Active TSS	HepG2	liver
3	chr5:74171800-74174800	Enhancers	Liver	Liver
4	chr5:74172000-74172600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:74172000-74172600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:74172000-74173800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:74172200-74172600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:74172200-74172600	Enhancers	H9 Cell Line	embryonic stem cell
9	chr5:74172200-74172600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:74172200-74172600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr5:74172200-74172600	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr5:74172200-74172600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr5:74172200-74173800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr5:74172200-74174000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:74172400-74173200	Enhancers	Brain Anterior Caudate	brain
16	chr5:74172400-74173200	Weak transcription	Brain Hippocampus Middle	brain
17	chr5:74172400-74173400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:74172400-74173400	Weak transcription	Brain Substantia Nigra	brain
19	chr5:74172400-74173800	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr5:74172400-74173800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:74172400-74174000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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