Variant report

Variant	rs1892253
Chromosome Location	chr6:25782314-25782315
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25778288..25781100-chr6:25781196..25783280,2	MCF-7	breast:
2	chr6:25780399..25781946-chr6:25782015..25783852,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10214468	0.92[CEU][hapmap]
rs1165168	0.93[CEU][hapmap]
rs1177441	0.92[CEU][hapmap]
rs1184498	0.93[CEU][hapmap]
rs13195279	0.85[CEU][hapmap]
rs13199775	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs13200921	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13207673	0.85[CEU][hapmap]
rs17586553	0.85[CEU][hapmap]
rs17587226	1.00[GIH][hapmap]
rs1892250	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1892251	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892252	0.86[CEU][hapmap]
rs1937126	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1954598	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28412066	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34351439	0.90[ASN][1000 genomes]
rs35436081	1.00[ASN][1000 genomes]
rs3734523	0.85[CEU][hapmap]
rs3949215	1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4236040	1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4712969	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs501220	0.93[CEU][hapmap]
rs523383	0.93[CEU][hapmap]
rs548987	0.93[CEU][hapmap]
rs555460	0.93[CEU][hapmap]
rs629444	0.85[CEU][hapmap]
rs6456701	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6902211	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6903766	1.00[GIH][hapmap]
rs6910549	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs6913795	0.90[ASN][1000 genomes]
rs6918310	1.00[CHB][hapmap]
rs6939997	1.00[CHB][hapmap]
rs6940007	0.85[CEU][hapmap]
rs6940698	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs7748167	0.85[CEU][hapmap]
rs7750960	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs9295675	0.85[CEU][hapmap]
rs9461216	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9461219	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs9461222	0.85[CEU][hapmap];0.88[MEX][hapmap]
rs9467600	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9467603	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9467606	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9467607	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9467609	1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs9467613	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9467621	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs9467622	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs9467623	0.90[ASN][1000 genomes]
rs9467626	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs9467635	0.85[CEU][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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv427747	chr6:25641380-25908218	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1892253	BTN3A2	cis	lymphoblastoid	GTEx
rs1892253	HLA-A	cis	multi-tissue	Pritchard
rs1892253	BTN3A2	cis	lymphoblastoid	seeQTL
rs1892253	BTN3A2	cis	multi-tissue	Pritchard

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25773800-25788600	Weak transcription	Pancreas	Pancrea
2	chr6:25780400-25798800	Weak transcription	Liver	Liver
3	chr6:25781000-25782400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:25781000-25786800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:25782000-25782400	Enhancers	HUES48 Cell Line	embryonic stem cell

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