Variant report

Variant	rs13219181
Chromosome Location	chr6:27136225-27136226
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27101946..27104264-chr6:27136179..27138427,2	MCF-7	breast:
2	chr6:27134929..27137913-chr6:27796376..27797878,2	MCF-7	breast:
3	chr6:27129652..27132851-chr6:27133864..27136225,4	MCF-7	breast:
4	chr6:27120589..27123058-chr6:27135123..27137850,2	MCF-7	breast:
5	chr6:27134151..27137360-chr6:27861915..27865428,4	MCF-7	breast:
6	chr6:27135834..27138150-chr6:27143711..27145656,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238610	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs13194053	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211901	0.82[AFR][1000 genomes]
rs34569203	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34783558	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3800307	0.82[AFR][1000 genomes]
rs3823427	0.87[YRI][hapmap]
rs4452638	0.85[CEU][hapmap]
rs4713074	0.81[YRI][hapmap]
rs5030956	0.82[YRI][hapmap]
rs61240102	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67330695	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67540232	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6904071	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs6913660	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914824	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934329	0.95[AMR][1000 genomes]
rs72842197	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7759741	0.81[YRI][hapmap]
rs926300	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs9468015	0.81[YRI][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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13219181	BTN2A1	Cis_1M	lymphoblastoid	RTeQTL
rs13219181	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs13219181	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27135600-27136400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr6:27135600-27136800	Enhancers	HSMMtube	muscle
3	chr6:27135600-27137000	Enhancers	NHDF-Ad	bronchial
4	chr6:27135600-27137000	Enhancers	NHLF	lung
5	chr6:27135600-27137200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:27135800-27137000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr6:27135800-27137000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:27135800-27137000	Enhancers	HUVEC	blood vessel
9	chr6:27135800-27137000	Enhancers	NHEK	skin
10	chr6:27135800-27137400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:27135800-27137400	Enhancers	K562	blood
12	chr6:27135800-27137600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:27136000-27136400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr6:27136000-27136600	Enhancers	A549	lung
15	chr6:27136000-27136800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:27136000-27136800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:27136000-27137000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr6:27136000-27137000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:27136000-27137200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:27136200-27136600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:27136200-27136800	Enhancers	HMEC	breast
22	chr6:27136200-27136800	Flanking Active TSS	Osteobl	bone
23	chr6:27136200-27137000	Enhancers	HSMM	muscle
24	chr6:27136200-27137000	Enhancers	NH-A	brain
25	chr6:27136200-27137400	Enhancers	Hela-S3	cervix

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