Variant report

Variant	rs12194741
Chromosome Location	chr6:73376868-73376869
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10455268	1.00[CHB][hapmap]
rs10484913	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10485213	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10498884	1.00[CHD][hapmap]
rs10943043	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10943045	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs10943048	1.00[ASN][1000 genomes]
rs10943050	1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943051	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs10943055	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10943057	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10943058	1.00[ASN][1000 genomes]
rs11758568	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11759937	1.00[ASN][1000 genomes]
rs12189933	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12189974	1.00[ASN][1000 genomes]
rs12190091	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12190092	0.84[EUR][1000 genomes]
rs12191039	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191216	1.00[ASN][1000 genomes]
rs12191848	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192751	1.00[ASN][1000 genomes]
rs12193274	0.83[CEU][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs12195259	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196826	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs12197962	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12199549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12200468	1.00[CHB][hapmap]
rs12200908	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12201380	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203288	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs12204139	1.00[CHB][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204989	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12205374	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12208053	1.00[CHB][hapmap]
rs12208907	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12210850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211580	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12212268	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12212419	0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212562	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12212818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214096	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs12214894	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12214895	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12215865	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12374630	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12374631	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17692715	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17692874	1.00[CHB][hapmap]
rs17692898	1.00[CHB][hapmap]
rs17729195	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[ASN][1000 genomes]
rs17749408	1.00[CHB][hapmap]
rs17749420	1.00[CHB][hapmap]
rs17796704	1.00[ASN][1000 genomes]
rs1928153	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34821312	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56086224	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62411986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411990	1.00[ASN][1000 genomes]
rs6453591	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[MEX][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6453592	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6453593	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6453594	0.82[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6928073	0.90[YRI][hapmap]
rs6931918	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6935174	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs719830	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs72935423	1.00[ASN][1000 genomes]
rs7748594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768673	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[MEX][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7772197	1.00[ASN][1000 genomes]
rs7776215	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9350467	0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023809	chr6:73157813-73477997	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv538303	chr6:73157813-73477997	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv3347486	chr6:73283590-73445976	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv1794408	chr6:73363298-73419987	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv463152	chr6:73369739-73406890	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv603692	chr6:73369739-73406890	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12194741	CD109	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73359600-73398800	Weak transcription	Primary B cells from peripheral blood	blood
2	chr6:73359800-73386800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:73362600-73379200	Weak transcription	Psoas Muscle	Psoas
4	chr6:73364400-73383200	Weak transcription	Primary B cells from cord blood	blood
5	chr6:73372000-73386800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:73376400-73377200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:73376800-73377200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin

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