Variant report

Variant	rs2198775
Chromosome Location	chr12:62236225-62236226
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:62235205..62237644-chr8:146126598..146128892,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196150	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10784255	0.82[EUR][1000 genomes]
rs10784256	0.82[EUR][1000 genomes]
rs10784257	0.83[EUR][1000 genomes]
rs10784258	0.82[EUR][1000 genomes]
rs10784259	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877723	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs10877724	0.88[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs10877725	0.81[EUR][1000 genomes]
rs10877727	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10877728	0.88[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs10877731	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877734	0.88[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877735	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877736	0.88[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877737	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877738	0.88[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877739	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877740	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11174141	0.88[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs11174148	0.88[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11174149	0.83[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11174150	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11174152	0.88[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11174157	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11174158	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11174160	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11174161	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11174176	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11608376	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11609198	0.90[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11609657	0.88[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11609916	0.82[EUR][1000 genomes]
rs11613304	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11614225	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11615924	0.83[EUR][1000 genomes]
rs12184468	0.85[ASN][1000 genomes]
rs12304279	0.88[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12367913	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12369048	0.87[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs12370254	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12371231	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12422512	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12423291	0.88[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs12423850	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12424350	0.88[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12578673	1.00[ASW][hapmap];0.88[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12579930	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12581090	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12581195	0.82[EUR][1000 genomes]
rs12581923	0.92[ASW][hapmap];0.88[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs12809540	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12809729	0.88[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12811649	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12811994	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12813599	0.88[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12814184	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12814204	1.00[ASW][hapmap];0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12815221	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12818281	0.80[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12821872	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12823193	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12826350	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12826571	0.84[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12827424	0.88[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs12828092	0.80[CEU][hapmap];0.86[ASN][1000 genomes]
rs12829322	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12830041	1.00[ASW][hapmap];0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap]
rs12831273	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17125407	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17577005	1.00[ASW][hapmap];0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs2061207	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2061208	0.89[CHB][hapmap];0.91[JPT][hapmap]
rs2067911	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs2198773	1.00[ASW][hapmap];0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs2198774	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2198780	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2198781	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2219259	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs2219260	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2359981	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2359982	0.88[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28672870	0.83[EUR][1000 genomes]
rs2884858	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2884859	0.89[CHB][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2884860	0.84[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34053266	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34586287	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34604177	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34810430	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34884798	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35378675	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35395140	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35406568	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35772232	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35785062	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35807037	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4482081	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4511327	0.88[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61942563	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61942566	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61942614	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61942620	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61942621	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6581424	0.88[CEU][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67880722	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67925612	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7132134	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7132727	0.88[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7137618	0.87[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs717271	0.88[CEU][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap]
rs724986	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs7294711	0.88[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs7306758	0.88[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73125574	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7315668	1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7484594	0.88[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7484623	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7484749	0.88[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7484947	0.88[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7485481	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7487085	0.88[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs7487661	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7488105	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7488993	0.82[EUR][1000 genomes]
rs7961924	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7968946	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7977604	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7979124	0.83[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7979223	0.93[CHB][hapmap];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039741	chr12:62046850-62491052	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2198775	CLCA2	trans	cerebellum	SCAN
rs2198775	OS9	cis	cerebellum	SCAN
rs2198775	R3HDM2	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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