Variant report

Variant	rs3094569
Chromosome Location	chr6:29483620-29483621
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29481318..29483910-chr6:29486622..29489549,2	K562	blood:

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs11968213	1.00[ASN][1000 genomes]
rs1233480	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1233493	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233494	0.87[EUR][1000 genomes]
rs1234844	0.87[EUR][1000 genomes]
rs2023463	0.87[EUR][1000 genomes]
rs2143668	0.89[EUR][1000 genomes]
rs2523431	0.89[EUR][1000 genomes]
rs2523432	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523443	0.89[EUR][1000 genomes]
rs2535231	1.00[ASN][1000 genomes]
rs2535234	1.00[ASN][1000 genomes]
rs2535247	1.00[ASN][1000 genomes]
rs2535248	1.00[ASN][1000 genomes]
rs2535250	1.00[ASN][1000 genomes]
rs2535251	1.00[ASN][1000 genomes]
rs2535252	1.00[ASN][1000 genomes]
rs2535255	1.00[ASN][1000 genomes]
rs2535256	1.00[ASN][1000 genomes]
rs2535257	1.00[ASN][1000 genomes]
rs2535259	1.00[ASN][1000 genomes]
rs2746149	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2746150	0.89[EUR][1000 genomes]
rs2747417	1.00[ASN][1000 genomes]
rs2747418	1.00[ASN][1000 genomes]
rs2747419	1.00[ASN][1000 genomes]
rs2747437	1.00[ASN][1000 genomes]
rs2747439	1.00[ASN][1000 genomes]
rs2747441	1.00[ASN][1000 genomes]
rs2747444	1.00[ASN][1000 genomes]
rs2747446	1.00[ASN][1000 genomes]
rs2747450	1.00[ASN][1000 genomes]
rs2747452	1.00[ASN][1000 genomes]
rs2747458	1.00[ASN][1000 genomes]
rs2747459	1.00[ASN][1000 genomes]
rs2747461	1.00[ASN][1000 genomes]
rs2747462	1.00[ASN][1000 genomes]
rs2747464	1.00[ASN][1000 genomes]
rs2747465	1.00[ASN][1000 genomes]
rs2747466	1.00[ASN][1000 genomes]
rs2857767	1.00[ASN][1000 genomes]
rs2857768	1.00[ASN][1000 genomes]
rs2857770	1.00[ASN][1000 genomes]
rs2857780	1.00[ASN][1000 genomes]
rs2857783	1.00[ASN][1000 genomes]
rs2857784	1.00[ASN][1000 genomes]
rs2907893	1.00[ASN][1000 genomes]
rs2907895	1.00[ASN][1000 genomes]
rs2907896	1.00[ASN][1000 genomes]
rs2982834	1.00[ASN][1000 genomes]
rs2982835	1.00[ASN][1000 genomes]
rs2982838	1.00[ASN][1000 genomes]
rs3117286	1.00[ASN][1000 genomes]
rs3117287	1.00[ASN][1000 genomes]
rs3117300	1.00[ASN][1000 genomes]
rs3117302	1.00[ASN][1000 genomes]
rs3117304	1.00[ASN][1000 genomes]
rs3117305	1.00[ASN][1000 genomes]
rs3117306	1.00[ASN][1000 genomes]
rs3117308	1.00[ASN][1000 genomes]
rs3117309	1.00[ASN][1000 genomes]
rs3117314	1.00[ASN][1000 genomes]
rs3117316	1.00[ASN][1000 genomes]
rs3129040	1.00[ASN][1000 genomes]
rs3129050	1.00[ASN][1000 genomes]
rs3129051	1.00[ASN][1000 genomes]
rs3129186	1.00[ASN][1000 genomes]
rs385743	1.00[ASN][1000 genomes]
rs387603	1.00[ASN][1000 genomes]
rs398931	1.00[ASN][1000 genomes]
rs404240	0.81[EUR][1000 genomes]
rs406424	1.00[ASN][1000 genomes]
rs408623	0.81[EUR][1000 genomes]
rs416560	1.00[ASN][1000 genomes]
rs422369	1.00[ASN][1000 genomes]
rs423281	1.00[ASN][1000 genomes]
rs423369	1.00[ASN][1000 genomes]
rs61730667	1.00[ASN][1000 genomes]
rs9468579	1.00[ASN][1000 genomes]
rs9468581	1.00[ASN][1000 genomes]
rs9500953	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3424039	chr6:29439297-29504564	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv883528	chr6:29447724-29494897	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv883529	chr6:29464365-29494897	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv966616	chr6:29479346-29495253	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3094569	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3094569	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3094569	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3094569	HLA-C	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29468600-29496200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:29478600-29483800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:29481600-29483800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:29483400-29484600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:29483400-29484800	Enhancers	HMEC	breast
6	chr6:29483600-29484400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:29483600-29484800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:29483600-29484800	Enhancers	NHEK	skin

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