Variant report

Variant	rs2451741
Chromosome Location	chr6:26629404-26629405
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26617539..26619687-chr6:26627974..26630970,2	K562	blood:
2	chr6:26595203..26596713-chr6:26627322..26630167,2	K562	blood:
3	chr6:26626416..26630175-chr6:26630389..26634346,5	K562	blood:

Variant related genes	Relation type
ENSG00000218346	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1021372	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1021373	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1027203	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1027204	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10484442	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[YRI][hapmap]
rs1056667	0.84[GIH][hapmap];0.80[LWK][hapmap];0.93[YRI][hapmap]
rs1078679	0.86[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[YRI][hapmap]
rs10946834	0.93[YRI][hapmap]
rs10946835	0.85[GIH][hapmap];0.81[LWK][hapmap];0.93[YRI][hapmap]
rs12526680	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13207371	0.84[EUR][1000 genomes]
rs1321479	0.82[GIH][hapmap];0.88[YRI][hapmap]
rs1321481	0.91[YRI][hapmap]
rs1321482	0.91[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[YRI][hapmap]
rs1490488	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1535276	0.85[GIH][hapmap];0.81[LWK][hapmap];0.89[YRI][hapmap]
rs1570059	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs1570060	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs1570061	0.91[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[YRI][hapmap]
rs1884946	0.93[YRI][hapmap]
rs1884947	0.81[CHB][hapmap]
rs2130657	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2172007	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2224380	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[YRI][hapmap]
rs2255070	0.89[YRI][hapmap]
rs2393670	0.85[GIH][hapmap];0.81[LWK][hapmap];0.93[YRI][hapmap]
rs2451711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2451712	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2451731	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451740	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2451744	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451750	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451751	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2494700	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2494701	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494703	0.81[CHD][hapmap]
rs2494709	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2494713	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2494716	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2498351	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2498380	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504565	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2504566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2504567	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2504571	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504592	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504599	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap]
rs2504600	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2758383	0.81[EUR][1000 genomes]
rs3001369	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34453863	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3736781	0.83[GIH][hapmap];0.81[LWK][hapmap];0.89[YRI][hapmap]
rs3736782	0.85[GIH][hapmap];0.81[LWK][hapmap];0.89[YRI][hapmap]
rs3800303	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4368798	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4713006	0.93[YRI][hapmap]
rs4713008	0.92[YRI][hapmap]
rs4871	0.85[GIH][hapmap];0.83[LWK][hapmap];0.93[YRI][hapmap]
rs62394558	0.82[EUR][1000 genomes]
rs6456733	0.86[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[YRI][hapmap]
rs6456735	0.90[JPT][hapmap];0.85[LWK][hapmap];0.93[YRI][hapmap]
rs6903973	0.84[GIH][hapmap];0.80[LWK][hapmap];0.89[YRI][hapmap]
rs6918360	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs6918506	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs6918854	0.91[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[YRI][hapmap]
rs6922824	0.86[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.84[YRI][hapmap]
rs6924865	0.82[GIH][hapmap];0.81[LWK][hapmap];0.93[YRI][hapmap]
rs6925087	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6925703	0.85[GIH][hapmap]
rs6925895	0.86[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[YRI][hapmap]
rs6926629	0.85[GIH][hapmap];0.81[LWK][hapmap];0.85[YRI][hapmap]
rs6930120	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs6933176	0.92[YRI][hapmap]
rs6941022	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[YRI][hapmap]
rs767471	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[YRI][hapmap]
rs7753565	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs7767847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9295695	0.85[GIH][hapmap];0.81[LWK][hapmap];0.93[YRI][hapmap]
rs9295701	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357010	0.85[GIH][hapmap];0.81[LWK][hapmap];0.93[YRI][hapmap]
rs9393729	0.85[GIH][hapmap];0.81[LWK][hapmap];0.93[YRI][hapmap]
rs9461270	0.85[GIH][hapmap];0.83[LWK][hapmap];0.93[YRI][hapmap]
rs9461271	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[YRI][hapmap]
rs9461272	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs9461273	0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9461275	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9461276	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9461288	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9467773	0.92[YRI][hapmap]
rs9467774	0.93[YRI][hapmap]
rs9467779	0.85[GIH][hapmap];0.80[LWK][hapmap];0.92[YRI][hapmap]
rs9467782	0.85[GIH][hapmap];0.83[LWK][hapmap];0.93[YRI][hapmap]
rs9467783	0.85[GIH][hapmap];0.83[LWK][hapmap];0.93[YRI][hapmap]
rs9467788	0.82[YRI][hapmap]
rs9467791	0.86[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[YRI][hapmap]
rs9467798	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs9467800	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs9467802	0.81[ASN][1000 genomes]
rs9467804	0.83[ASN][1000 genomes]
rs9467805	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9467810	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9467813	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9986382	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs2451741	BTN3A1	cis	cerebellum	SCAN
rs2451741	ZNF322	cis	Nerve Tibial	GTEx
rs2451741	HMGN4	Cis_1M	lymphoblastoid	RTeQTL
rs2451741	ZNF322	cis	Artery Tibial	GTEx
rs2451741	ZNF204P	cis	cerebellum	SCAN
rs2451741	HCG11	Cis_1M	lymphoblastoid	RTeQTL
rs2451741	ZNF322A	cis	multi-tissue	Pritchard
rs2451741	RP11-457M11.2	cis	lung	GTEx
rs2451741	BTN3A3	cis	cerebellum	SCAN
rs2451741	ZNF322	cis	Thyroid	GTEx
rs2451741	BTN3A3	cis	parietal	SCAN
rs2451741	BTN3A2	cis	cerebellum	SCAN
rs2451741	ZNF204P	cis	parietal	SCAN
rs2451741	RP11-457M11.2	cis	Thyroid	GTEx
rs2451741	RP11-457M11.2	cis	Nerve Tibial	GTEx
rs2451741	ZNF322B	trans	lymphoblastoid	seeQTL
rs2451741	RP11-457M11.2	cis	Artery Tibial	GTEx
rs2451741	HMGN4	cis	lesional skin	skin_eQTL
rs2451741	ZNF322B	trans	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26625400-26639200	Weak transcription	Brain Hippocampus Middle	brain
2	chr6:26629400-26639200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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