Variant report

Variant	rs12058085
Chromosome Location	chr1:224880669-224880670
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224874309..224876593-chr1:224880376..224882878,2	K562	blood:
2	chr1:224873427..224876593-chr1:224880376..224882893,3	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1036431	0.85[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1039265	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10495227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915691	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10915693	0.85[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10915695	0.85[CEU][hapmap];0.87[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11805320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12060334	0.85[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12062831	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12065840	0.85[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12068125	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12072810	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12073052	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12077707	0.84[CEU][hapmap]
rs12079156	0.80[EUR][1000 genomes]
rs12088524	0.87[ASW][hapmap];0.85[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12092532	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12562581	0.93[CEU][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12565092	0.80[EUR][1000 genomes]
rs12567125	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1337538	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1465766	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1465767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16850786	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4363402	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61603030	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61827113	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61827152	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6426147	0.85[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6695864	0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs7541279	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7554310	0.85[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12058085	PYCR2	cis	cerebellum	SCAN
rs12058085	RAB3GAP2	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224832200-224884400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:224862400-224902000	Weak transcription	Pancreas	Pancrea
3	chr1:224871800-224884600	Weak transcription	Fetal Brain Female	brain
4	chr1:224873000-224884800	Weak transcription	NHLF	lung
5	chr1:224873400-224884200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:224875000-224881600	Weak transcription	NH-A	brain
7	chr1:224875600-224888400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:224876200-224881200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:224876400-224881800	Weak transcription	NHDF-Ad	bronchial
10	chr1:224877400-224884000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:224877600-224891600	Weak transcription	Dnd41	blood
12	chr1:224878800-224884200	Weak transcription	Fetal Brain Male	brain
13	chr1:224879000-224884000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:224879400-224884200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:224880000-224881000	Weak transcription	Ovary	ovary
16	chr1:224880400-224881000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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