Variant report

Variant	rs12563301
Chromosome Location	chr1:174060062-174060063
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:174059895-174060229	T-47D	breast:	n/a	n/a

Variant related genes	Relation type
RPL30P1	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10158115	0.80[EUR][1000 genomes]
rs10158289	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10798301	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs10798302	0.87[CHB][hapmap]
rs10912734	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12066153	0.87[CHB][hapmap]
rs12079062	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12079063	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12079820	0.88[CEU][hapmap];0.88[MEX][hapmap]
rs12085290	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12087441	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12094341	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12691474	0.88[CEU][hapmap]
rs1322780	0.91[CHB][hapmap];0.81[CHD][hapmap]
rs16846683	0.87[CHB][hapmap]
rs1799876	0.95[CHB][hapmap]
rs1884994	0.83[CHB][hapmap]
rs1951627	0.87[CHB][hapmap]
rs2064149	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2143114	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2294492	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2860847	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2901785	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4442420	0.88[CEU][hapmap];0.92[MEX][hapmap]
rs4650945	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4650989	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs4650990	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs4652169	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4652234	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4652237	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4652274	0.88[CEU][hapmap];0.88[MEX][hapmap]
rs4652294	0.87[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57919173	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5877	0.85[CHB][hapmap]
rs5878	0.91[CHB][hapmap]
rs60354115	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6425274	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6425275	0.87[CHB][hapmap]
rs6656188	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6658543	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6663875	0.91[CHB][hapmap];0.81[CHD][hapmap]
rs6665484	0.87[CHB][hapmap]
rs6667267	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs6670617	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs6672986	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6677660	0.87[CHB][hapmap]
rs6681390	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6681618	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6686083	0.87[CHB][hapmap]
rs6689285	0.87[CHB][hapmap]
rs6690570	0.85[EUR][1000 genomes]
rs6695327	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs6695636	0.81[EUR][1000 genomes]
rs6696076	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6696163	0.87[CHB][hapmap]
rs6699146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs714624	0.87[CHB][hapmap]
rs7413166	0.86[CHB][hapmap]
rs7512930	0.80[EUR][1000 genomes]
rs7523460	0.80[EUR][1000 genomes]
rs7526024	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7533430	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7537517	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs7552830	0.80[EUR][1000 genomes]
rs7553788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7555067	0.81[EUR][1000 genomes]
rs941989	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs972361	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs9787001	0.86[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	nsv916960	chr1:173907804-174080248	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	nsv465661	chr1:174014507-174152688	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv548193	chr1:174014507-174152688	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12563301	RC3H1	Cis_1M	lymphoblastoid	RTeQTL
rs12563301	RC3H1	cis	normal skin	skin_eQTL
rs12563301	MRPS14	cis	parietal	SCAN
rs12563301	PRDX6	cis	parietal	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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