Variant report

Variant	rs1925400
Chromosome Location	chr1:67352960-67352961
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:67351495..67353743-chr1:67373492..67375346,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1104705	0.82[MKK][hapmap]
rs11208966	0.84[MKK][hapmap]
rs11208968	0.83[MKK][hapmap]
rs12045569	0.82[MKK][hapmap]
rs12239035	0.88[CEU][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12239074	0.88[CEU][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1280338	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1925399	0.94[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1925401	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1925402	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1925403	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1925404	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1925405	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1925406	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1931297	0.94[CEU][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2147835	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2147836	0.83[CEU][hapmap]
rs269399	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs269401	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs269402	0.94[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs269403	0.88[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs269405	0.82[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2991353	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2991354	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2991359	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4255358	0.80[EUR][1000 genomes]
rs55858354	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56400880	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs573490	0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61467716	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6699606	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72671675	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72671677	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72671679	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72671680	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72671682	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72671685	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7552770	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[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	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv546443	chr1:67268642-67352960	Genic enhancers Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv871738	chr1:67268642-67375206	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv871259	chr1:67275027-67375206	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1925400	WLS	cis	parietal	SCAN
rs1925400	MIER1	cis	parietal	SCAN
rs1925400	LRRC40	cis	parietal	SCAN
rs1925400	GADD45A	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67346800-67363200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:67348400-67389000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:67349400-67389600	Weak transcription	Aorta	Aorta
4	chr1:67350000-67369400	Weak transcription	Fetal Kidney	kidney
5	chr1:67352200-67372600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:67352800-67385600	Weak transcription	Ovary	ovary

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