Variant report

Variant	rs12373827
Chromosome Location	chr2:101043669-101043670
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:101040106..101042486-chr2:101042782..101044958,2	MCF-7	breast:
2	chr2:101023081..101025478-chr2:101042210..101044979,2	MCF-7	breast:
3	chr2:101041152..101044058-chr2:101179314..101180934,2	K562	blood:
4	chr2:101033457..101036653-chr2:101042804..101046394,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115539	Chromatin interaction
ENSG00000115526	Chromatin interaction
ENSG00000238029	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10048665	0.81[EUR][1000 genomes]
rs10174145	0.83[EUR][1000 genomes]
rs10182399	0.83[EUR][1000 genomes]
rs10183150	0.87[EUR][1000 genomes]
rs10186134	0.91[EUR][1000 genomes]
rs10193204	0.90[EUR][1000 genomes]
rs10202326	0.82[EUR][1000 genomes]
rs1030901	0.90[EUR][1000 genomes]
rs1030902	0.86[EUR][1000 genomes]
rs11123826	0.84[EUR][1000 genomes]
rs1114595	0.90[EUR][1000 genomes]
rs11674569	0.85[CEU][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs11674830	0.87[EUR][1000 genomes]
rs11675901	0.82[EUR][1000 genomes]
rs11678148	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs11678158	0.83[EUR][1000 genomes]
rs11680660	0.83[EUR][1000 genomes]
rs11682557	0.81[EUR][1000 genomes]
rs11683088	0.83[EUR][1000 genomes]
rs11684004	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs11684516	0.83[EUR][1000 genomes]
rs11685250	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs11685406	0.82[EUR][1000 genomes]
rs11686649	0.82[EUR][1000 genomes]
rs11686799	0.83[EUR][1000 genomes]
rs11686842	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs11686880	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs11688285	0.81[EUR][1000 genomes]
rs11691135	0.83[EUR][1000 genomes]
rs11693471	0.81[EUR][1000 genomes]
rs11694642	0.83[EUR][1000 genomes]
rs11694700	0.84[EUR][1000 genomes]
rs11892034	0.84[EUR][1000 genomes]
rs12617779	0.84[EUR][1000 genomes]
rs12618908	0.81[EUR][1000 genomes]
rs12621892	0.81[EUR][1000 genomes]
rs12989897	0.84[EUR][1000 genomes]
rs12991172	0.84[EUR][1000 genomes]
rs12991577	0.86[EUR][1000 genomes]
rs12997725	0.82[EUR][1000 genomes]
rs12999151	0.84[EUR][1000 genomes]
rs13021801	0.82[EUR][1000 genomes]
rs13026570	0.84[EUR][1000 genomes]
rs13031711	0.84[EUR][1000 genomes]
rs13031906	0.84[EUR][1000 genomes]
rs1437967	0.86[EUR][1000 genomes]
rs1437969	0.93[EUR][1000 genomes]
rs1530029	0.84[EUR][1000 genomes]
rs1530030	0.85[CEU][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs1530031	0.89[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs1811415	0.85[EUR][1000 genomes]
rs1837143	0.90[EUR][1000 genomes]
rs2099611	0.92[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs2164847	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2241809	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs2241810	0.85[CEU][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs2241811	0.92[CEU][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs2309798	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2309800	0.81[CEU][hapmap];0.92[EUR][1000 genomes]
rs2309852	0.84[EUR][1000 genomes]
rs3748930	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs3828193	0.92[CEU][hapmap];0.80[JPT][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs4149505	0.88[EUR][1000 genomes]
rs4149507	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs4149510	0.92[CEU][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs4149512	0.92[CEU][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs4149513	0.92[CEU][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs4149517	0.92[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs4149518	0.89[CEU][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs4149523	0.93[EUR][1000 genomes]
rs4264577	0.81[EUR][1000 genomes]
rs4340543	0.90[EUR][1000 genomes]
rs4378827	0.90[EUR][1000 genomes]
rs4387816	0.84[EUR][1000 genomes]
rs4407265	0.92[EUR][1000 genomes]
rs4477940	0.83[EUR][1000 genomes]
rs4640404	0.93[EUR][1000 genomes]
rs4850927	0.83[EUR][1000 genomes]
rs4850929	0.81[CEU][hapmap];0.93[EUR][1000 genomes]
rs4850930	0.81[CEU][hapmap];0.93[EUR][1000 genomes]
rs4850931	0.89[EUR][1000 genomes]
rs4851288	0.83[EUR][1000 genomes]
rs4851294	0.84[EUR][1000 genomes]
rs4851298	0.82[EUR][1000 genomes]
rs4851302	0.82[EUR][1000 genomes]
rs4851303	0.91[EUR][1000 genomes]
rs4851304	0.84[EUR][1000 genomes]
rs4851310	0.84[EUR][1000 genomes]
rs4851311	0.84[EUR][1000 genomes]
rs4851312	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs4851313	0.93[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4851315	0.80[JPT][hapmap]
rs62148360	0.85[EUR][1000 genomes]
rs6542940	0.91[EUR][1000 genomes]
rs6542942	0.87[EUR][1000 genomes]
rs6542944	0.81[CEU][hapmap];0.93[EUR][1000 genomes]
rs6542947	0.93[EUR][1000 genomes]
rs6716636	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs6725052	0.84[EUR][1000 genomes]
rs6731549	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs6736311	0.82[EUR][1000 genomes]
rs6737217	0.86[EUR][1000 genomes]
rs6749018	0.91[EUR][1000 genomes]
rs6754176	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs6757754	0.82[EUR][1000 genomes]
rs74177694	0.84[EUR][1000 genomes]
rs7585582	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs7590388	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7597615	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs893416	0.80[EUR][1000 genomes]
rs930374	0.90[EUR][1000 genomes]
rs9973536	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv916792	chr2:101021066-101525200	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv582532	chr2:101029002-101531943	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1011990	chr2:101039956-101105648	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12373827	LONRF2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:101034800-101043800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:101041000-101044400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr2:101043000-101044400	Enhancers	Monocytes-CD14+_RO01746	blood

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