Variant report

Variant	rs12044025
Chromosome Location	chr1:76249715-76249716
allele	A/C
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	CBX3	chr1:76249379-76250715	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:
2	chr1:76187424..76195796-chr1:76248839..76258922,52	K562	blood:

Variant related genes	Relation type
SNORD45C	TF binding region
RABGGTB	TF binding region
SNORD45A	TF binding region
ENSG00000178193	Chromatin interaction
ENSG00000117054	Chromatin interaction

Extended variants
information (count: 144 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs1021462	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10732724	0.83[JPT][hapmap]
rs10782556	0.89[ASN][1000 genomes]
rs10873738	1.00[JPT][hapmap]
rs10873804	0.86[JPT][hapmap]
rs11161439	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161447	0.87[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs11161465	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11161600	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161602	0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11161605	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11161731	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs11161852	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs11161887	0.91[JPT][hapmap]
rs11164015	0.85[EUR][1000 genomes]
rs11164035	0.83[CEU][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11164037	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1144328	0.91[JPT][hapmap]
rs1144331	0.91[JPT][hapmap]
rs1144333	0.91[JPT][hapmap]
rs1144337	0.91[JPT][hapmap]
rs1144342	0.91[JPT][hapmap]
rs1146647	0.90[JPT][hapmap]
rs1146648	0.95[JPT][hapmap]
rs1146649	0.91[JPT][hapmap]
rs1146651	0.95[JPT][hapmap]
rs1146652	0.91[JPT][hapmap]
rs12021750	0.87[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs12022011	0.94[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12024645	0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12027620	0.91[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12031600	0.88[ASN][1000 genomes]
rs12032051	0.87[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs12033058	0.87[CHB][hapmap];0.96[JPT][hapmap];0.89[ASN][1000 genomes]
rs12033059	0.89[ASN][1000 genomes]
rs12034697	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12044211	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs12045299	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12045363	0.89[ASN][1000 genomes]
rs12049212	0.88[ASN][1000 genomes]
rs12076093	0.95[JPT][hapmap]
rs12090712	0.95[JPT][hapmap]
rs12401729	0.86[JPT][hapmap]
rs12404553	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12407107	0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12409592	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs12410373	0.86[JPT][hapmap]
rs1250876	0.90[JPT][hapmap]
rs1250880	0.86[JPT][hapmap]
rs1251079	0.81[JPT][hapmap]
rs1251272	0.95[JPT][hapmap]
rs1251274	0.91[JPT][hapmap]
rs12563737	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12564772	0.89[ASN][1000 genomes]
rs12567390	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs12703	0.91[JPT][hapmap]
rs12724860	0.85[ASN][1000 genomes]
rs12727156	0.81[ASN][1000 genomes]
rs12728962	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12732495	0.86[JPT][hapmap]
rs12732722	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12736447	0.83[EUR][1000 genomes]
rs12744608	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12745456	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12747967	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12756349	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12757213	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12757866	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1303870	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1391518	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1391520	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1463812	0.81[CEU][hapmap]
rs1498313	0.95[JPT][hapmap]
rs1535740	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1591120	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1603734	0.96[JPT][hapmap]
rs1689271	0.86[JPT][hapmap]
rs17097634	0.89[ASN][1000 genomes]
rs17097681	0.83[JPT][hapmap]
rs17097695	0.83[JPT][hapmap]
rs17649675	0.87[JPT][hapmap]
rs1796812	0.82[JPT][hapmap]
rs1826978	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1908089	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2047435	0.81[JPT][hapmap]
rs211713	0.85[CEU][hapmap]
rs211719	0.85[CEU][hapmap]
rs2131558	0.89[ASN][1000 genomes]
rs2307077	0.91[JPT][hapmap]
rs34486572	0.89[ASN][1000 genomes]
rs35290302	0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs35837767	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3737574	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3765682	0.86[JPT][hapmap]
rs3795251	0.86[JPT][hapmap]
rs3819949	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs5745314	0.87[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs5745327	0.91[JPT][hapmap]
rs5745334	0.87[CHB][hapmap];0.96[JPT][hapmap];0.89[ASN][1000 genomes]
rs5745343	0.91[JPT][hapmap]
rs5745352	1.00[YRI][hapmap]
rs5745353	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5745354	0.86[JPT][hapmap]
rs5745368	1.00[YRI][hapmap]
rs5745392	0.91[JPT][hapmap]
rs5745426	0.87[ASN][1000 genomes]
rs5745429	0.86[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs5745448	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs5745451	0.91[JPT][hapmap]
rs5745464	0.86[JPT][hapmap]
rs5745465	0.86[JPT][hapmap]
rs5745523	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs5745532	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs5745542	0.83[JPT][hapmap]
rs5745546	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs58552356	0.87[ASN][1000 genomes]
rs6665431	0.82[ASN][1000 genomes]
rs6668963	0.81[ASN][1000 genomes]
rs6676182	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6680389	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6687882	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs6695055	0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67108483	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71502708	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71656856	0.81[ASN][1000 genomes]
rs7417486	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7514912	0.95[JPT][hapmap]
rs7516477	0.90[JPT][hapmap]
rs7525919	0.87[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7545057	0.86[JPT][hapmap]
rs7548391	0.96[JPT][hapmap]
rs7548695	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7548991	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7552289	0.81[CEU][hapmap]
rs814875	0.90[CEU][hapmap]
rs814876	0.85[CEU][hapmap]
rs815301	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs815304	0.83[EUR][1000 genomes]
rs815305	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9660848	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[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
rs12044025	RABGGTB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 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
5	chr1:76249200-76251200	Weak transcription	Right Atrium	heart
6	chr1:76249600-76253200	Active TSS	GM12878-XiMat	blood

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