Variant report

Variant	rs2489314
Chromosome Location	chr1:225108778-225108779
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224831768..224834375-chr1:225108469..225110982,2	K562	blood:

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10158926	0.84[AMR][1000 genomes]
rs1080260	0.98[EUR][1000 genomes]
rs10915779	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1110378	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1110379	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12067806	0.87[CHB][hapmap]
rs12563434	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1436176	0.82[JPT][hapmap]
rs1506069	0.94[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1506071	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1506072	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1506074	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1832540	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1936631	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2014656	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2014667	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2051158	0.92[ASN][1000 genomes]
rs2128268	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2128270	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs2244102	0.91[ASN][1000 genomes]
rs2244126	0.91[ASN][1000 genomes]
rs2254158	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2254406	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2406097	1.00[CEU][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449256	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2449258	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2449269	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449281	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2449287	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2449304	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2449315	1.00[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2449320	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2449322	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2456336	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2456341	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2456349	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2489296	0.87[AMR][1000 genomes]
rs2489298	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2489301	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2489303	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2489311	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489313	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2489324	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2489327	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2489337	0.83[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2489343	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2489346	0.91[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2489348	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2489352	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2489353	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2489355	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2501078	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2501082	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501083	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501085	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501087	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501099	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2501100	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2501101	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2501107	0.87[CHB][hapmap]
rs2501108	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2501110	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2501120	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2501133	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2501147	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2501151	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2662917	0.82[JPT][hapmap]
rs2929626	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2939363	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3101904	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3101910	0.81[AMR][1000 genomes]
rs3101916	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3101917	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3102106	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3102115	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3105558	0.87[CHB][hapmap]
rs3105564	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3105565	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs3105572	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3120987	0.84[AMR][1000 genomes]
rs3120989	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3120991	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3120993	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3128654	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3128655	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3128657	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3128658	0.87[CHB][hapmap];0.94[CHD][hapmap]
rs3128664	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3128666	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3128667	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57137890	0.84[AMR][1000 genomes]
rs59420435	0.84[AMR][1000 genomes]
rs61211002	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61849768	0.84[ASN][1000 genomes]
rs6426163	0.94[JPT][hapmap];0.84[AMR][1000 genomes]
rs6686694	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6697382	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7530659	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7548138	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs981067	0.87[CHB][hapmap]
rs995613	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757773	chr1:225087924-225253274	Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv2759001	chr1:225087924-225253274	Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2489314	CAPN2	cis	cerebellum	SCAN
rs2489314	TMEM63A	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225102400-225110000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:225107400-225110000	Weak transcription	Dnd41	blood
3	chr1:225107600-225108800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr1:225107600-225110000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:225108000-225109200	Weak transcription	Liver	Liver
6	chr1:225108600-225110000	Weak transcription	Pancreas	Pancrea

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