Variant report

Variant	rs13195040
Chromosome Location	chr6:27413924-27413925
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	chr6:27411742..27414316-chr6:27438239..27440962,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000096654	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10484399	0.90[CEU][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs13191227	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13191474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13195636	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs13196692	0.92[EUR][1000 genomes]
rs13202775	0.83[EUR][1000 genomes]
rs13207689	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs13209332	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs13218537	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28360634	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34071253	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34105070	0.83[EUR][1000 genomes]
rs34196306	0.96[EUR][1000 genomes]
rs34332556	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34573979	0.94[EUR][1000 genomes]
rs34613987	0.87[EUR][1000 genomes]
rs34864796	0.87[EUR][1000 genomes]
rs34953377	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34965299	0.91[EUR][1000 genomes]
rs35120058	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35716472	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35848276	0.91[EUR][1000 genomes]
rs35984974	0.91[EUR][1000 genomes]
rs41269265	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56401801	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58616630	0.94[EUR][1000 genomes]
rs66785117	0.91[EUR][1000 genomes]
rs66841633	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67240003	0.87[EUR][1000 genomes]
rs67859638	0.91[EUR][1000 genomes]
rs6904596	0.87[EUR][1000 genomes]
rs6918792	0.86[EUR][1000 genomes]
rs71537559	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72839477	0.87[EUR][1000 genomes]
rs7749305	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs7757148	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1031803	chr6:27355881-27423655	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv538166	chr6:27355881-27423655	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs13195040	BTN3A3	cis	lymphoblastoid	seeQTL
rs13195040	HLA-A	cis	multi-tissue	Pritchard
rs13195040	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs13195040	HLA-H	cis	multi-tissue	Pritchard
rs13195040	BTN3A2	cis	multi-tissue	Pritchard
rs13195040	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs13195040	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs13195040	BTN3A2	trans	lymphoblastoid	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27407400-27414200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr6:27411200-27417600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr6:27412600-27438000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:27413000-27415600	Weak transcription	HSMMtube	muscle
5	chr6:27413400-27414000	Weak transcription	Left Ventricle	heart
6	chr6:27413400-27418000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:27413600-27417800	Weak transcription	Fetal Heart	heart
8	chr6:27413600-27425600	ZNF genes & repeats	Fetal Brain Female	brain

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