Variant report

Variant	rs3799383
Chromosome Location	chr6:26510748-26510749
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26507087..26510972-chr6:26516270..26519753,3	MCF-7	breast:
2	chr6:26342168..26345048-chr6:26509847..26512007,2	MCF-7	breast:
3	chr6:26501363..26503070-chr6:26510004..26512764,2	K562	blood:
4	chr6:26510097..26511884-chr6:26513965..26515676,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199289	Chromatin interaction
ENSG00000124557	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 28 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10484443	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs11967935	0.82[ASN][1000 genomes]
rs12173854	0.92[CEU][hapmap]
rs12174602	0.85[CEU][hapmap]
rs12174631	0.81[CEU][hapmap]
rs12176129	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12176317	0.85[CEU][hapmap]
rs13195047	0.90[ASN][1000 genomes]
rs13210025	0.86[JPT][hapmap]
rs13214027	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13216828	0.85[CEU][hapmap]
rs16891717	0.85[ASN][1000 genomes]
rs16891725	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16891790	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs16901784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1977	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs1978	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs1979	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs2072803	0.85[CEU][hapmap];0.89[CHB][hapmap];0.85[EUR][1000 genomes]
rs2072806	0.85[CEU][hapmap];0.89[CHB][hapmap];0.85[EUR][1000 genomes]
rs2073529	0.85[CEU][hapmap]
rs2073531	0.84[CEU][hapmap]
rs2076030	0.85[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes]
rs2093169	0.92[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.98[ASN][1000 genomes]
rs2235251	0.89[EUR][1000 genomes]
rs2295593	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2393667	0.85[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.89[EUR][1000 genomes]
rs34273322	0.86[EUR][1000 genomes]
rs34313099	0.90[ASN][1000 genomes]
rs35942482	0.89[EUR][1000 genomes]
rs3734544	0.92[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.84[ASN][1000 genomes]
rs3757150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[ASN][1000 genomes]
rs3999471	0.92[JPT][hapmap]
rs4634439	0.93[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs56296968	0.85[ASN][1000 genomes]
rs66823108	0.80[EUR][1000 genomes]
rs67234939	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68072215	0.80[EUR][1000 genomes]
rs6900118	0.89[CHB][hapmap]
rs6900665	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6911765	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs6920256	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72841536	0.80[EUR][1000 genomes]
rs7740197	0.92[JPT][hapmap]
rs7756567	0.85[ASN][1000 genomes]
rs7759969	0.84[JPT][hapmap]
rs7773938	0.92[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.85[ASN][1000 genomes]
rs9295702	0.92[JPT][hapmap]
rs9348709	0.84[CEU][hapmap]
rs9348712	0.85[CEU][hapmap]
rs9348716	0.85[CEU][hapmap]
rs9348718	1.00[CHB][hapmap]
rs9348719	0.85[ASN][1000 genomes]
rs9348720	0.85[ASN][1000 genomes]
rs9348721	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9358932	0.85[CEU][hapmap]
rs9358934	0.85[CEU][hapmap]
rs9358935	0.85[CEU][hapmap]
rs9358937	0.85[CEU][hapmap]
rs9358938	0.84[CEU][hapmap];0.89[CHB][hapmap];0.85[EUR][1000 genomes]
rs9358939	0.86[EUR][1000 genomes]
rs9358944	0.92[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.85[ASN][1000 genomes]
rs9358945	0.92[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.92[YRI][hapmap];0.85[ASN][1000 genomes]
rs9358946	0.92[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.85[ASN][1000 genomes]
rs9358947	0.85[ASN][1000 genomes]
rs9358948	0.85[ASN][1000 genomes]
rs9358950	0.81[ASN][1000 genomes]
rs9366653	0.85[CEU][hapmap]
rs9366655	0.80[EUR][1000 genomes]
rs9366656	0.85[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.89[EUR][1000 genomes]
rs9366658	0.92[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.85[ASN][1000 genomes]
rs9379851	0.85[CEU][hapmap]
rs9379855	0.85[CEU][hapmap]
rs9379856	0.85[CEU][hapmap]
rs9379857	0.85[CEU][hapmap]
rs9379858	0.85[CEU][hapmap]
rs9379859	0.85[CEU][hapmap]
rs9379864	0.85[CEU][hapmap]
rs9379873	0.86[EUR][1000 genomes]
rs9379875	0.85[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.89[EUR][1000 genomes]
rs9379880	0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9379882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379883	0.90[ASN][1000 genomes]
rs9379884	0.90[ASN][1000 genomes]
rs9379888	0.88[ASN][1000 genomes]
rs9379893	0.92[JPT][hapmap]
rs9379895	0.92[JPT][hapmap]
rs9379897	0.93[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs9379899	0.93[CEU][hapmap];0.92[JPT][hapmap]
rs9379907	0.92[JPT][hapmap]
rs9393705	0.85[CEU][hapmap]
rs9393706	0.85[CEU][hapmap]
rs9393707	0.85[CEU][hapmap]
rs9393708	0.85[CEU][hapmap]
rs9393710	0.85[CEU][hapmap]
rs9393713	0.85[CEU][hapmap]
rs9393718	0.85[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes]
rs9393721	0.89[CHB][hapmap]
rs9393725	0.82[ASN][1000 genomes]
rs9393727	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393735	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9393737	0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
4	nsv482836	chr6:26352883-26520964	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:28)

SNP	Gene	Cis/trans	Tissue	Source
rs3799383	BTN3A2	cis	Esophagus Mucosa	GTEx
rs3799383	ZSCAN23	cis	cerebellum	SCAN
rs3799383	BTN3A2	cis	cerebellum	SCAN
rs3799383	ZNF192	cis	cerebellum	SCAN
rs3799383	BTN3A2	cis	Whole Blood	GTEx
rs3799383	ZKSCAN3	cis	parietal	SCAN
rs3799383	BTN3A2	cis	lymphoblastoid	GTEx
rs3799383	BTN3A2	cis	Thyroid	GTEx
rs3799383	HIST1H4L	cis	parietal	SCAN
rs3799383	BTN3A3	cis	lymphoblastoid	seeQTL
rs3799383	BTN3A2	cis	Muscle Skeletal	GTEx
rs3799383	CMAH	cis	parietal	SCAN
rs3799383	BTN3A2	cis	Heart Left Ventricle	GTEx
rs3799383	BTN3A2	cis	lymphoblastoid	seeQTL
rs3799383	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs3799383	BTN3A2	cis	Esophagus Muscularis	GTEx
rs3799383	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs3799383	BTN3A2	cis	lesional skin	skin_eQTL
rs3799383	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs3799383	LRRC16A	cis	parietal	SCAN
rs3799383	BTN3A2	cis	normal skin	skin_eQTL
rs3799383	BTN3A2	cis	uninvolved skin	skin_eQTL
rs3799383	HIST1H2BD	cis	cerebellum	SCAN
rs3799383	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs3799383	ZSCAN23	cis	parietal	SCAN
rs3799383	BTN3A2	cis	Artery Tibial	GTEx
rs3799383	BTN3A2	cis	Nerve Tibial	GTEx
rs3799383	BTN3A2	cis	lung	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26505600-26520600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:26508200-26513200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:26510600-26510800	Enhancers	HepG2	liver

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