Variant report

Variant	rs2309798
Chromosome Location	chr2:100956949-100956950
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100944968..100947303-chr2:100956166..100958150,2	MCF-7	breast:
2	chr2:100944547..100946729-chr2:100956360..100957899,2	MCF-7	breast:
3	chr2:100932853..100934904-chr2:100954615..100957367,2	K562	blood:
4	chr2:100937318..100939314-chr2:100955169..100957159,2	MCF-7	breast:
5	chr2:100937601..100941206-chr2:100954662..100959386,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170500	Chromatin interaction

Extended variants
information (count: 162 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:158)

rs_ID	r²[population]
rs10048665	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10170109	0.89[AMR][1000 genomes]
rs10174145	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10180423	0.84[CEU][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10182399	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10183150	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10186134	0.90[EUR][1000 genomes]
rs10193204	0.92[EUR][1000 genomes]
rs10194210	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10195793	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10202326	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1030901	0.92[EUR][1000 genomes]
rs1030902	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10460478	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11123824	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11123826	0.96[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11123827	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1114595	0.91[EUR][1000 genomes]
rs11674569	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11674830	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11675901	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676282	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11677524	0.80[AMR][1000 genomes]
rs11678148	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678158	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11680660	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11682557	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11682748	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11683088	0.83[EUR][1000 genomes]
rs11683121	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11684004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11684516	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685406	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11686293	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11686649	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11686799	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11686842	1.00[CEU][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11686880	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11687352	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11687864	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11687865	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11688285	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689439	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11691135	0.89[CEU][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11691684	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11693044	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11693424	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11693471	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694642	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11694700	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11892034	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11895772	0.88[EUR][1000 genomes]
rs12373827	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs12615466	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12617779	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12618908	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621892	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622318	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12712075	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12989897	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990688	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12991172	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12991577	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12997725	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12999151	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12999779	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13001423	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13006224	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13020451	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13021801	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13023534	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13026570	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13031711	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13031906	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1437967	0.86[EUR][1000 genomes]
rs1437969	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1530028	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1530029	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1530030	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1530031	0.92[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs1811415	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1837143	0.91[EUR][1000 genomes]
rs1866198	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1946799	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1967339	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1967340	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1967341	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2099611	0.82[CEU][hapmap];0.81[CHD][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs2164847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241809	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2241810	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2241811	0.82[CEU][hapmap];0.81[CHD][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs2309800	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2309852	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3748930	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs3828193	0.89[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs4149505	0.92[EUR][1000 genomes]
rs4149507	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4149510	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4149512	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4149513	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4149517	0.82[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs4149518	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4149523	0.88[EUR][1000 genomes]
rs4264577	0.96[CEU][hapmap];0.84[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4340543	0.92[EUR][1000 genomes]
rs4378827	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4387816	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4407265	0.86[EUR][1000 genomes]
rs4477940	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4635546	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4640404	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4850927	0.92[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4850929	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs4850930	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs4850931	0.92[EUR][1000 genomes]
rs4851288	0.83[EUR][1000 genomes]
rs4851292	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4851293	0.87[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4851294	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4851297	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4851298	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851300	1.00[ASN][1000 genomes]
rs4851302	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851303	0.89[EUR][1000 genomes]
rs4851304	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851305	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4851310	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851311	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851312	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs4851313	0.81[EUR][1000 genomes]
rs4851315	0.85[JPT][hapmap]
rs62148360	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6542940	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6542942	0.92[EUR][1000 genomes]
rs6542944	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs6542947	0.88[EUR][1000 genomes]
rs6716636	1.00[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6725052	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6731549	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6736311	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6737217	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6749018	0.89[EUR][1000 genomes]
rs6754176	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs6757754	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74177694	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74177695	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs74177696	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7425449	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7425797	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7585582	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs7597615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893416	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs920269	0.84[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs920270	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs930374	0.89[EUR][1000 genomes]
rs9973536	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv834311	chr2:100816917-100990036	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2309798	LONRF2	cis	cerebellum	SCAN
rs2309798	INPP4A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100956800-100967200	Weak transcription	Gastric	stomach

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