Variant report

Variant	rs2060570
Chromosome Location	chr12:29607931-29607932
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10771535	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10771537	0.84[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10843424	0.90[ASN][1000 genomes]
rs10843425	0.88[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10843426	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1347570	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1436317	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1436318	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2043623	0.88[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2350530	0.88[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6487822	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7296963	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][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	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv898952	chr12:29565537-29617550	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2060570	RP11-996F15.2	cis	Thyroid	GTEx
rs2060570	YARS2	cis	parietal	SCAN
rs2060570	RP11-996F15.2	cis	lung	GTEx
rs2060570	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs2060570	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs2060570	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29581800-29613600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr12:29584200-29641800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:29588000-29639800	Weak transcription	Aorta	Aorta
4	chr12:29594200-29614000	Weak transcription	Left Ventricle	heart
5	chr12:29598400-29657400	Weak transcription	HSMM	muscle
6	chr12:29600000-29639800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr12:29600600-29675600	Weak transcription	Psoas Muscle	Psoas
8	chr12:29604200-29655400	Weak transcription	Adipose Nuclei	Adipose
9	chr12:29605000-29613600	Weak transcription	HSMMtube	muscle
10	chr12:29607200-29608400	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr12:29607200-29609800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:29607400-29608000	Enhancers	Brain Substantia Nigra	brain
13	chr12:29607600-29608000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:29607600-29608000	Enhancers	Brain Cingulate Gyrus	brain
15	chr12:29607600-29608400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:29607600-29609200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr12:29607800-29608000	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr12:29607800-29608000	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr12:29607800-29608800	Enhancers	Cortex derived primary cultured neurospheres	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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