Variant report

Variant	rs12129172
Chromosome Location	chr1:210344911-210344912
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10746423	0.86[AMR][1000 genomes]
rs10779523	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10779525	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779526	0.95[EUR][1000 genomes]
rs1099863	0.82[AMR][1000 genomes]
rs11119376	0.82[AMR][1000 genomes]
rs11119425	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11119427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119428	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119429	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1334567	0.87[AMR][1000 genomes]
rs1334568	0.86[AMR][1000 genomes]
rs1387933	0.88[AMR][1000 genomes]
rs1413695	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1490419	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs170557	0.81[AMR][1000 genomes]
rs1933477	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs227169	0.84[AMR][1000 genomes]
rs227172	0.92[AMR][1000 genomes]
rs227174	0.88[AMR][1000 genomes]
rs227179	0.88[AMR][1000 genomes]
rs227181	0.81[AMR][1000 genomes]
rs227182	0.81[AMR][1000 genomes]
rs227191	0.85[AMR][1000 genomes]
rs227193	0.85[AMR][1000 genomes]
rs227196	0.84[AMR][1000 genomes]
rs227197	0.81[AMR][1000 genomes]
rs227201	0.82[AMR][1000 genomes]
rs227203	0.82[AMR][1000 genomes]
rs227204	0.86[AMR][1000 genomes]
rs227205	0.86[AMR][1000 genomes]
rs227209	0.89[AMR][1000 genomes]
rs227211	0.86[AMR][1000 genomes]
rs227217	0.83[AMR][1000 genomes]
rs227218	0.84[AMR][1000 genomes]
rs227219	0.84[AMR][1000 genomes]
rs227224	0.81[AMR][1000 genomes]
rs227230	0.81[AMR][1000 genomes]
rs2484032	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2484034	0.89[LWK][hapmap];0.83[MKK][hapmap]
rs2485890	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2485891	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485892	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485893	0.95[EUR][1000 genomes]
rs2485894	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2494168	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494189	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2494190	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2494191	0.87[AFR][1000 genomes]
rs2636376	0.88[AMR][1000 genomes]
rs2743889	0.88[AMR][1000 genomes]
rs4421592	0.82[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4844947	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4844954	1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs6540580	0.86[AMR][1000 genomes]
rs6540584	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6656855	0.87[AMR][1000 genomes]
rs701947	0.89[CHD][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.88[AMR][1000 genomes]
rs701948	0.89[CHD][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.84[AMR][1000 genomes]
rs7514257	0.81[AMR][1000 genomes]
rs7519750	0.87[AMR][1000 genomes]
rs7525980	0.81[AMR][1000 genomes]
rs7528647	0.83[AMR][1000 genomes]
rs7529352	0.89[CHD][hapmap]
rs7541569	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7547709	0.81[AMR][1000 genomes]
rs846551	0.85[AMR][1000 genomes]
rs846552	0.85[AMR][1000 genomes]
rs846554	0.86[AMR][1000 genomes]
rs846555	0.86[AMR][1000 genomes]
rs9659395	0.87[AMR][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	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv873144	chr1:210252522-210347417	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv873145	chr1:210302595-210347417	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv873146	chr1:210312760-210347417	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12129172	CR1	cis	parietal	SCAN
rs12129172	DYRK3	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210339400-210361200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:210343400-210345000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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