Variant report

Variant	rs1883259
Chromosome Location	chr6:25683280-25683281
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25678273..25680918-chr6:25683099..25686089,2	MCF-7	breast:
2	chr6:25678136..25680692-chr6:25682799..25684594,2	K562	blood:
3	chr6:25682123..25685911-chr6:25693985..25696713,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000217408	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1012899	0.90[CHB][hapmap];0.86[CHD][hapmap]
rs1074706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1074707	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs1474595	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs169946	0.84[CEU][hapmap]
rs1980453	0.90[CHB][hapmap]
rs2010291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2011465	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2011472	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs212930	0.84[CEU][hapmap]
rs212938	0.84[CEU][hapmap]
rs212941	0.84[CEU][hapmap]
rs214049	0.83[CEU][hapmap]
rs214050	0.84[CEU][hapmap]
rs214066	0.84[CEU][hapmap];0.81[GIH][hapmap]
rs2328889	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3804102	0.86[JPT][hapmap]
rs391629	0.84[CEU][hapmap]
rs4383809	0.85[EUR][1000 genomes]
rs4576241	0.84[CEU][hapmap]
rs4711090	0.83[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456685	0.85[EUR][1000 genomes]
rs6900762	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6903257	0.84[CEU][hapmap]
rs6932536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs721803	0.90[CHB][hapmap]
rs909664	0.91[ASN][1000 genomes]
rs926326	0.84[CEU][hapmap]
rs932319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9393654	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs969297	0.84[CEU][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	nsv883488	chr6:25592489-25731691	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1883259	BTN3A2	cis	lymphoblastoid	seeQTL
rs1883259	BTN3A2	cis	multi-tissue	Pritchard
rs1883259	HIST1H2AH	cis	parietal	SCAN
rs1883259	HIST1H2BD	cis	lymphoblastoid	seeQTL
rs1883259	ABT1	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25683000-25685200	Weak transcription	K562	blood
2	chr6:25683000-25689600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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