Variant report

Variant	rs10861299
Chromosome Location	chr12:105358968-105358969
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105355342..105357518-chr12:105358674..105361105,2	K562	blood:
2	chr12:105354302..105359267-chr12:105378860..105381853,4	MCF-7	breast:
3	chr12:105358306..105359021-chr7:75988024..75988532,2	Hela-S3	cervix:
4	chr12:105358604..105363045-chr12:105378560..105382753,4	MCF-7	breast:
5	chr12:105351015..105355585-chr12:105357288..105360893,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151131	Chromatin interaction
ENSG00000136052	Chromatin interaction
ENSG00000170027	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10778361	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10778363	0.89[ASN][1000 genomes]
rs10861298	0.85[CEU][hapmap]
rs10861301	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861302	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10861303	0.96[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10861304	0.92[ASN][1000 genomes]
rs10861308	0.89[ASN][1000 genomes]
rs10861309	0.89[ASN][1000 genomes]
rs10861310	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10861311	0.89[ASN][1000 genomes]
rs10861313	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11112263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11112284	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11112286	0.93[ASN][1000 genomes]
rs11112287	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11112296	0.92[ASN][1000 genomes]
rs11112297	0.93[ASN][1000 genomes]
rs11112299	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11112306	0.91[ASN][1000 genomes]
rs1129593	0.95[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap]
rs12581510	0.89[ASN][1000 genomes]
rs12581542	0.88[ASN][1000 genomes]
rs16890	0.91[ASN][1000 genomes]
rs17036612	0.89[ASN][1000 genomes]
rs4281549	0.89[ASN][1000 genomes]
rs4318051	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4331189	0.92[ASN][1000 genomes]
rs4473015	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4964119	0.89[YRI][hapmap]
rs6539176	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7134342	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7297572	0.89[ASN][1000 genomes]
rs7302931	0.92[ASN][1000 genomes]
rs7304326	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7308025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7308266	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7308568	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7308574	0.89[ASN][1000 genomes]
rs7309375	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7311995	0.89[ASN][1000 genomes]
rs73387268	0.89[ASN][1000 genomes]
rs7958263	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7970173	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10861299	C12orf45	cis	Lymphoblastoid	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105356600-105359400	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr12:105357400-105359000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:105358600-105359000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:105358800-105360000	Enhancers	GM12878-XiMat	blood

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