Variant report

Variant	rs1036950
Chromosome Location	chr1:75866662-75866663
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10747387	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10874264	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10874305	0.88[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10874311	0.82[JPT][hapmap]
rs1107148	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1116878	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs1249784	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1249786	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12738260	0.82[JPT][hapmap]
rs1343519	0.88[CHB][hapmap];0.84[CHD][hapmap];0.89[ASN][1000 genomes]
rs1343520	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs1858627	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1858628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs1889036	0.83[JPT][hapmap]
rs1936358	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2347214	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2587042	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6593575	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6675276	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]

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	esv3368999	chr1:75524762-75933220	Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1013952	chr1:75716654-75936048	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv535004	chr1:75716654-75936048	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1036950	SNORD45B	cis	cerebellum	SCAN
rs1036950	SLC44A5	cis	Skin Sun Exposed Lower leg	GTEx
rs1036950	SLC44A5	cis	Thyroid	GTEx
rs1036950	SLC44A5	cis	Muscle Skeletal	GTEx
rs1036950	HEBP2	trans	lymphoblastoid	seeQTL
rs1036950	TYW3	cis	parietal	SCAN
rs1036950	SLC44A5	cis	normal skin	skin_eQTL
rs1036950	CRYZ	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75866400-75866800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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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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