Variant report

Variant	rs9461219
Chromosome Location	chr6:25836927-25836928
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25831276..25833219-chr6:25835965..25837963,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124568	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs10484433	0.85[MEX][hapmap]
rs10484435	0.82[CEU][hapmap]
rs13191445	0.91[CEU][hapmap]
rs13192713	0.82[CEU][hapmap]
rs13195279	0.86[AMR][1000 genomes]
rs13198474	0.91[CEU][hapmap]
rs13199775	1.00[CEU][hapmap];1.00[CHB][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]
rs13200921	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201341	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs13202688	0.91[CEU][hapmap]
rs13207673	1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs13211947	0.91[CEU][hapmap]
rs13212534	0.89[CEU][hapmap];0.82[MEX][hapmap]
rs13213957	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs13220488	0.86[AMR][1000 genomes]
rs16891235	0.85[MEX][hapmap]
rs17526722	0.85[CEU][hapmap]
rs17587226	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs1892250	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892251	0.90[ASN][1000 genomes]
rs1892253	0.90[ASN][1000 genomes]
rs1937126	0.90[ASN][1000 genomes]
rs1954598	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28412066	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34351439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35169013	0.86[AMR][1000 genomes]
rs35436081	0.90[ASN][1000 genomes]
rs3734523	1.00[MEX][hapmap]
rs3734528	0.85[MEX][hapmap]
rs3949215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4236040	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712969	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456701	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67554133	1.00[AMR][1000 genomes]
rs68194335	1.00[AMR][1000 genomes]
rs6902211	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910549	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs6913795	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918310	1.00[CHB][hapmap]
rs6939997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6940007	1.00[MEX][hapmap]
rs6940698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750960	1.00[CHB][hapmap]
rs9461216	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467600	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467603	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467606	1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467607	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9467613	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467623	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467632	0.86[AMR][1000 genomes]
rs972087	0.91[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	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
4	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs9461219	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs9461219	HLA-A	cis	multi-tissue	Pritchard
rs9461219	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs9461219	BTN3A3	cis	lymphoblastoid	seeQTL
rs9461219	BTN3A2	cis	Muscle Skeletal	GTEx
rs9461219	HIST1H2BD	cis	lymphoblastoid	seeQTL
rs9461219	BTN3A2	cis	multi-tissue	Pritchard
rs9461219	BTN3A2	cis	Whole Blood	GTEx
rs9461219	BTN3A2	cis	Esophagus Muscularis	GTEx
rs9461219	HIST1H2AC	cis	lymphoblastoid	seeQTL
rs9461219	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs9461219	BTN3A2	cis	lymphoblastoid	GTEx
rs9461219	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs9461219	BTN3A2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25835200-25837600	Enhancers	Fetal Intestine Small	intestine
2	chr6:25835400-25837200	Enhancers	Fetal Intestine Large	intestine
3	chr6:25835800-25837600	Flanking Active TSS	HepG2	liver
4	chr6:25836400-25838000	Weak transcription	Aorta	Aorta
5	chr6:25836600-25852000	Weak transcription	Liver	Liver

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