Variant report

Variant	rs1233708
Chromosome Location	chr6:28173219-28173220
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28170074..28175450-chr6:28180913..28183647,5	K562	blood:
2	chr6:28169001..28171000-chr6:28171450..28173526,2	K562	blood:
3	chr6:28109242..28110938-chr6:28172802..28175131,2	MCF-7	breast:
4	chr6:28172570..28175998-chr6:28183959..28188768,7	K562	blood:
5	chr6:28154709..28159711-chr6:28172250..28177968,6	K562	blood:
6	chr6:28166299..28169743-chr6:28173090..28175496,4	K562	blood:

Variant related genes	Relation type
ENSG00000198315	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000218016	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1071893	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150666	0.91[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1150678	0.85[EUR][1000 genomes]
rs1225592	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1225595	0.84[CHB][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1225716	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1233691	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233699	0.82[ASW][hapmap]
rs1233701	0.88[ASW][hapmap]
rs1233704	0.88[ASW][hapmap]
rs1237875	0.88[ASW][hapmap]
rs149897	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs149942	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs149944	0.95[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs149945	0.95[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs149955	0.95[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs149959	0.95[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs149972	0.95[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs149989	0.95[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap]
rs156739	0.95[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs1631552	0.95[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1770131	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17711801	0.81[CEU][hapmap]
rs183244	0.86[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs188105	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs203876	0.95[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs203877	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs203882	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs203883	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs203884	0.95[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs203892	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs203893	0.95[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2622315	0.83[YRI][hapmap]
rs2622319	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2791332	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs476167	0.82[EUR][1000 genomes]
rs536704	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9295760	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9461443	0.91[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	nsv883514	chr6:28155418-28185726	Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv883515	chr6:28156476-28181675	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv883516	chr6:28156476-28185726	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs1233708	BTN3A2	cis	multi-tissue	Pritchard
rs1233708	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs1233708	ZNF323	cis	Temporal Cortex	GTEx
rs1233708	ZNF323	cis	Frontal Cortex	GTEx
rs1233708	RP1-265C24.5	cis	Muscle Skeletal	GTEx
rs1233708	ZNF323	cis	Brain Pons	GTEx
rs1233708	AL022393.7	cis	Heart Left Ventricle	GTEx
rs1233708	AL022393.7	cis	Nerve Tibial	GTEx
rs1233708	IRAK3	trans	brain	seeQTL
rs1233708	AL022393.7	cis	Muscle Skeletal	GTEx
rs1233708	ZNF323	cis	Cerebellum	GTEx
rs1233708	OR2B8P	cis	Thyroid	GTEx
rs1233708	ZSCAN31	cis	Thyroid	GTEx
rs1233708	AL022393.7	cis	Artery Tibial	GTEx
rs1233708	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28172800-28173400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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