Variant report

Variant	rs12756349
Chromosome Location	chr1:76246238-76246239
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10782556	0.94[ASN][1000 genomes]
rs11161439	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11161447	0.85[ASN][1000 genomes]
rs11161465	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11161600	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161602	0.96[ASN][1000 genomes]
rs11161605	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11161704	0.82[ASN][1000 genomes]
rs11161790	0.81[ASN][1000 genomes]
rs11161795	0.81[ASN][1000 genomes]
rs11164015	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11164035	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11164037	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1144328	0.82[ASN][1000 genomes]
rs1144331	0.82[ASN][1000 genomes]
rs1144333	0.82[ASN][1000 genomes]
rs1144337	0.82[ASN][1000 genomes]
rs1144339	0.82[ASN][1000 genomes]
rs1144341	0.82[ASN][1000 genomes]
rs1144342	0.82[ASN][1000 genomes]
rs1146587	0.82[ASN][1000 genomes]
rs1146645	0.82[ASN][1000 genomes]
rs1146647	0.82[ASN][1000 genomes]
rs1146649	0.82[ASN][1000 genomes]
rs1146651	0.82[ASN][1000 genomes]
rs1146652	0.82[ASN][1000 genomes]
rs12021750	0.86[ASN][1000 genomes]
rs12022011	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12024086	0.81[ASN][1000 genomes]
rs12024645	0.94[ASN][1000 genomes]
rs12024786	0.81[ASN][1000 genomes]
rs12027620	0.87[ASN][1000 genomes]
rs12031600	0.90[ASN][1000 genomes]
rs12032051	0.86[ASN][1000 genomes]
rs12033058	0.94[ASN][1000 genomes]
rs12033059	0.94[ASN][1000 genomes]
rs12034697	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12044025	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12045299	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12045363	0.94[ASN][1000 genomes]
rs12049212	0.90[ASN][1000 genomes]
rs12401729	0.81[ASN][1000 genomes]
rs12403889	0.81[ASN][1000 genomes]
rs12404553	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12407107	0.94[ASN][1000 genomes]
rs1250876	0.81[ASN][1000 genomes]
rs1250880	0.80[ASN][1000 genomes]
rs1250882	0.82[ASN][1000 genomes]
rs1251077	0.81[ASN][1000 genomes]
rs1251270	0.82[ASN][1000 genomes]
rs1251273	0.82[ASN][1000 genomes]
rs1251274	0.82[ASN][1000 genomes]
rs12563737	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12564772	0.94[ASN][1000 genomes]
rs12703	0.82[ASN][1000 genomes]
rs12724860	0.89[ASN][1000 genomes]
rs12727156	0.86[ASN][1000 genomes]
rs12728962	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12732722	0.84[ASN][1000 genomes]
rs12736447	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12744608	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12745456	0.80[ASN][1000 genomes]
rs12747967	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12757213	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12757866	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1391518	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1391520	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1535740	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1591120	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17097634	0.94[ASN][1000 genomes]
rs1767457	0.83[ASN][1000 genomes]
rs1826978	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2012536	0.82[ASN][1000 genomes]
rs2131558	0.94[ASN][1000 genomes]
rs34486572	0.94[ASN][1000 genomes]
rs34984955	0.81[ASN][1000 genomes]
rs35290302	0.90[ASN][1000 genomes]
rs35837767	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3737574	0.93[ASN][1000 genomes]
rs5745314	0.94[ASN][1000 genomes]
rs5745327	0.82[ASN][1000 genomes]
rs5745334	0.94[ASN][1000 genomes]
rs5745343	0.82[ASN][1000 genomes]
rs5745353	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5745354	0.82[ASN][1000 genomes]
rs5745392	0.82[ASN][1000 genomes]
rs5745426	0.89[ASN][1000 genomes]
rs5745429	0.90[ASN][1000 genomes]
rs58552356	0.92[ASN][1000 genomes]
rs61676733	0.81[ASN][1000 genomes]
rs6665431	0.84[ASN][1000 genomes]
rs6668963	0.83[ASN][1000 genomes]
rs6676182	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6680389	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6695055	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67108483	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71502708	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71656856	0.86[ASN][1000 genomes]
rs7417486	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7516477	0.80[ASN][1000 genomes]
rs7525919	0.94[ASN][1000 genomes]
rs7548695	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7548991	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs815301	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs815304	0.84[EUR][1000 genomes]
rs815305	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9660848	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][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	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830281	chr1:76095292-76251053	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12756349	RABGGTB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76227400-76249800	Weak transcription	Primary B cells from peripheral blood	blood
2	chr1:76241400-76251000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:76241400-76251200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:76244400-76250800	Weak transcription	HepG2	liver

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