Variant report

Variant	rs10861300
Chromosome Location	chr12:105368036-105368037
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10861312	0.83[EUR][1000 genomes]
rs11112268	1.00[ASN][1000 genomes]
rs11112269	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12230563	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4310692	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4964119	0.96[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs4964309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4964318	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6539173	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6539174	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6539178	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6539179	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6539180	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7134013	0.83[EUR][1000 genomes]
rs7138144	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7299739	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs7307234	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7975396	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv869	chr12:105363425-105394904	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	nsv983361	chr12:105367672-105376203	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3436359	chr12:105367822-105372020	Weak transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10861300	SLC5A8	cis	cerebellum	SCAN
rs10861300	GNPTAB	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105365200-105368600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr12:105365400-105368200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:105365600-105368400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:105365800-105368200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:105365800-105368400	Weak transcription	Osteobl	bone
6	chr12:105365800-105368600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:105365800-105368600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr12:105367000-105368200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:105367000-105368600	Enhancers	Placenta	Placenta
10	chr12:105367800-105368400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:105368000-105368200	Enhancers	GM12878-XiMat	blood
12	chr12:105368000-105368200	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr12:105368000-105368800	Flanking Active TSS	NHEK	skin
14	chr12:105368000-105369000	Enhancers	Stomach Mucosa	stomach
15	chr12:105368000-105370800	Enhancers	HMEC	breast
16	chr12:105368000-105371800	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr12:105368000-105371800	Enhancers	Primary B cells from peripheral blood	blood

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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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