Variant report

Variant	rs1600130
Chromosome Location	chr12:10454496-10454497
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	chr12:10453243..10455277-chr12:10460503..10462364,2	K562	blood:

Variant related genes	Relation type
ENSG00000134539	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11053738	0.82[EUR][1000 genomes]
rs11053739	0.91[EUR][1000 genomes]
rs11053740	0.91[EUR][1000 genomes]
rs11611333	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs12829155	0.92[CEU][hapmap]
rs1600126	0.83[EUR][1000 genomes]
rs2302489	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs2537752	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs2537781	0.96[CEU][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617146	0.96[CEU][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs3759270	0.89[CEU][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs3759272	0.89[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs3759273	0.89[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs3809214	0.92[CEU][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs3867486	0.89[EUR][1000 genomes]
rs3912117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3927994	0.92[EUR][1000 genomes]
rs4764341	0.81[TSI][hapmap]
rs61242400	0.91[EUR][1000 genomes]
rs7135494	0.83[EUR][1000 genomes]
rs7301715	0.84[EUR][1000 genomes]
rs7313418	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs7314888	0.92[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs7316530	0.84[EUR][1000 genomes]
rs7961687	0.81[TSI][hapmap]
rs7964452	0.82[EUR][1000 genomes]
rs7970821	0.85[TSI][hapmap]
rs7972782	0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832328	chr12:10398071-10620443	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv605	chr12:10448638-10494208	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1600130	SLC2A3	cis	cerebellum	SCAN
rs1600130	NOP2	cis	cerebellum	SCAN
rs1600130	ATN1	cis	parietal	SCAN
rs1600130	APOLD1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10447400-10455000	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr12:10447800-10456600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:10453200-10461000	Weak transcription	Placenta	Placenta
4	chr12:10453400-10454600	Enhancers	Thymus	Thymus
5	chr12:10453400-10457000	Enhancers	Placenta Amnion	Placenta Amnion
6	chr12:10453600-10454600	Enhancers	Primary T cells from cord blood	blood
7	chr12:10453800-10457200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:10454200-10458000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr12:10454400-10455600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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