Variant report

Variant	rs7780746
Chromosome Location	chr7:21846551-21846552
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1011950	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1018918	1.00[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs10226098	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs10226244	0.90[EUR][1000 genomes]
rs10230246	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10233760	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10239296	1.00[CEU][hapmap]
rs10254975	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10255013	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10256263	0.95[CEU][hapmap]
rs10258448	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs10265592	0.88[JPT][hapmap]
rs10270774	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10277757	0.96[CEU][hapmap];0.97[TSI][hapmap]
rs10807808	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs10950875	0.96[CEU][hapmap];0.88[CHD][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10950878	1.00[CEU][hapmap]
rs10950879	0.96[CEU][hapmap]
rs12700308	1.00[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs13231851	1.00[CEU][hapmap]
rs17145488	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1962775	1.00[CEU][hapmap]
rs1962776	1.00[CEU][hapmap]
rs2014193	1.00[CEU][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs2072093	0.83[EUR][1000 genomes]
rs2189023	1.00[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs2214325	1.00[CEU][hapmap]
rs2214326	1.00[CEU][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs34540475	0.81[EUR][1000 genomes]
rs35471448	0.81[EUR][1000 genomes]
rs35922142	0.81[EUR][1000 genomes]
rs3735522	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4141347	1.00[CEU][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs4582443	0.96[CEU][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs4722059	0.83[CEU][hapmap]
rs6461602	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6954167	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6954728	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6969900	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7780479	0.92[CEU][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7787438	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7788531	0.96[CEU][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7792944	1.00[CEU][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs7801909	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs7803777	0.85[EUR][1000 genomes]
rs7804316	0.92[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9638792	0.91[EUR][1000 genomes]
rs9639398	0.92[CEU][hapmap];0.93[EUR][1000 genomes]

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	nsv1018133	chr7:21740118-22055283	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases
2	nsv830922	chr7:21793386-21964675	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv933320	chr7:21840543-21882825	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7780746	IL6	cis	parietal	SCAN
rs7780746	C7orf46	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21834400-21848600	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr7:21845000-21846600	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr7:21845600-21847000	Enhancers	Liver	Liver

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