Variant report

Variant	rs7140164
Chromosome Location	chr14:39685539-39685540
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	chr14:39644203..39647101-chr14:39685504..39687288,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259083	Chromatin interaction
ENSG00000100941	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10131617	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10133417	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs10134365	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10136285	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10136309	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10137352	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs10137905	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs10138869	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10149495	0.94[EUR][1000 genomes]
rs10151659	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10162550	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs10872920	0.86[JPT][hapmap]
rs11157053	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs11157058	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs11620695	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs11621330	0.86[JPT][hapmap]
rs11626679	0.88[JPT][hapmap]
rs11627580	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs12434140	0.86[JPT][hapmap]
rs12587713	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs12894855	0.82[JPT][hapmap]
rs1594842	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs17109021	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs17109028	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs17109073	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs1897792	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs1950952	0.86[JPT][hapmap]
rs1998194	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2082635	0.86[JPT][hapmap]
rs2093217	0.94[EUR][1000 genomes]
rs2274396	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs2274399	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4902528	0.82[JPT][hapmap]
rs4902569	0.81[JPT][hapmap]
rs4902570	0.81[JPT][hapmap]
rs6571906	0.96[ASN][1000 genomes]
rs6571919	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7143393	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7143646	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7145048	0.94[ASN][1000 genomes]
rs7145343	0.96[ASN][1000 genomes]
rs7145345	0.96[ASN][1000 genomes]
rs7146289	0.96[ASN][1000 genomes]
rs7148150	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs7151608	0.82[JPT][hapmap]
rs7153482	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs7156264	1.00[CEU][hapmap];0.83[JPT][hapmap];0.94[EUR][1000 genomes]
rs7157271	0.97[ASN][1000 genomes]
rs7160180	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74048714	0.94[EUR][1000 genomes]
rs74048717	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8004716	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs8009490	0.97[ASN][1000 genomes]
rs8011619	0.80[ASN][1000 genomes]
rs8018717	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs956109	0.82[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1246	chr14:39656597-39701520	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1053133	chr14:39657535-39770729	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv977460	chr14:39684663-39690168	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7140164	BRMS1L	cis	cerebellum	SCAN
rs7140164	CTAGE5	cis	parietal	SCAN
rs7140164	SEC23A	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39674000-39705400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr14:39681600-39686600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr14:39681800-39686400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr14:39681800-39686400	Weak transcription	HUVEC	blood vessel
5	chr14:39682000-39686400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr14:39682000-39686400	Weak transcription	A549	lung
7	chr14:39682000-39686400	Weak transcription	HMEC	breast
8	chr14:39682000-39686400	Weak transcription	NHEK	skin
9	chr14:39685200-39687400	Enhancers	Hela-S3	cervix

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