Variant report

Variant	rs734642
Chromosome Location	chr5:127248485-127248486
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	chr5:127247758..127249668-chr5:127252486..127255400,2	MCF-7	breast:
2	chr5:127241157..127248623-chr5:127417759..127421019,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245937	Chromatin interaction
ENSG00000064651	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10036951	0.86[EUR][1000 genomes]
rs10491255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13155003	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13166824	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13187008	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs151848	0.93[ASN][1000 genomes]
rs151850	0.93[ASN][1000 genomes]
rs151851	0.94[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs151852	0.93[ASN][1000 genomes]
rs17164526	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17164533	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17164534	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17839667	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2176831	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs245161	0.95[ASN][1000 genomes]
rs245162	0.93[ASN][1000 genomes]
rs245166	0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs245168	0.93[ASN][1000 genomes]
rs245169	0.93[ASN][1000 genomes]
rs245170	0.93[ASN][1000 genomes]
rs4836339	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58316019	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62375865	0.93[ASN][1000 genomes]
rs7702027	0.81[EUR][1000 genomes]
rs7708799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7723029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9327454	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9327455	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[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
rs734642	SLC12A2	cis	parietal	SCAN
rs734642	HINT1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127245600-127249200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr5:127246400-127249800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:127247000-127252400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr5:127248200-127248600	Enhancers	Small Intestine	intestine
5	chr5:127248200-127248600	Enhancers	Stomach Mucosa	stomach
6	chr5:127248400-127249600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:127248400-127252400	Weak transcription	Rectal Mucosa Donor 31	rectum

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