Variant report

Variant	rs246739
Chromosome Location	chr7:140687173-140687174
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	chr7:140686234..140687769-chr7:140687897..140689543,2	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10240888	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10255167	0.86[ASN][1000 genomes]
rs10268118	0.82[ASN][1000 genomes]
rs10281975	0.80[EUR][1000 genomes]
rs1044927	0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs10488098	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1089264	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10952364	0.86[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs12538296	0.93[ASN][1000 genomes]
rs13234490	0.88[CHB][hapmap]
rs13236704	0.88[CHB][hapmap]
rs13438418	0.80[EUR][1000 genomes]
rs13438609	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1476816	0.88[CHB][hapmap]
rs1476868	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs16882367	0.88[ASN][1000 genomes]
rs17622717	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17623204	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17695341	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17695623	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17695707	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17695935	1.00[CEU][hapmap];0.85[AFR][1000 genomes]
rs17695995	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1968140	1.00[CEU][hapmap];0.92[AFR][1000 genomes]
rs2079827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688430	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3805116	0.85[JPT][hapmap]
rs3852286	0.82[ASN][1000 genomes]
rs3864527	0.82[ASN][1000 genomes]
rs38715	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs38717	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs38718	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs38719	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs38720	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs38722	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs38723	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs38726	0.89[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38730	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs38731	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs38734	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38736	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38739	0.89[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs38740	0.89[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41282721	0.92[AFR][1000 genomes]
rs4726225	0.88[CHB][hapmap]
rs488795	0.88[CHB][hapmap]
rs512509	0.88[CHB][hapmap]
rs55720380	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs557962	0.88[CHB][hapmap]
rs55875248	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs56055746	0.92[AFR][1000 genomes]
rs56347011	0.88[EUR][1000 genomes]
rs57143942	0.80[EUR][1000 genomes]
rs57675404	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs57846481	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs58901822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59183598	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs59232128	0.84[EUR][1000 genomes]
rs59477283	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs59816436	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs60081231	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs60164573	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60251368	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62484288	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62484291	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62484294	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62484295	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62484299	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62484300	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62485366	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62485368	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62485369	0.80[EUR][1000 genomes]
rs62485370	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62485372	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62485377	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62485379	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62485383	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62485390	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62485391	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62485451	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62485452	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62485453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6464217	0.88[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs6662	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6971577	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs7801518	0.88[CHB][hapmap]
rs7810757	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs801117	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs801121	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs801127	0.88[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9274	0.88[CHB][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	nsv1017980	chr7:140601863-140721368	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1030195	chr7:140615828-140746345	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1026448	chr7:140636599-140716829	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs246739	BRAF	Cis_1M	lymphoblastoid	RTeQTL
rs246739	MRPS33	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140686400-140688000	Weak transcription	HepG2	liver
2	chr7:140686800-140688400	Weak transcription	Fetal Intestine Large	intestine

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