Variant report

Variant	rs10876008
Chromosome Location	chr12:39126750-39126751
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10506124	0.85[ASN][1000 genomes]
rs10506125	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs10506126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10506127	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10783317	0.86[JPT][hapmap]
rs10783329	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783330	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875953	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875954	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876005	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11169006	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169054	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11169087	0.88[JPT][hapmap]
rs11169100	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169189	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169222	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169258	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169482	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs11169518	0.88[CEU][hapmap]
rs11169519	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs11169535	0.92[CEU][hapmap]
rs12229104	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12231313	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12300353	0.86[AMR][1000 genomes]
rs12314639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12424190	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12818797	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12822023	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12831609	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1352121	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1386018	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1564978	0.88[JPT][hapmap]
rs1586373	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs1875609	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2220267	0.86[JPT][hapmap]
rs34311455	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35254764	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3759139	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3803020	1.00[YRI][hapmap]
rs3887436	0.89[CEU][hapmap]
rs4616077	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61937754	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7309400	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7312879	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7315271	0.84[CEU][hapmap];0.82[AMR][1000 genomes]
rs7316392	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7960616	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7971075	0.88[JPT][hapmap]
rs7979541	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9325144	0.85[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	nsv469356	chr12:38242029-39187408	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv558574	chr12:38242029-39187408	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv1039538	chr12:38640895-39180750	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10876008	ALG10B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39056000-39168600	Weak transcription	Hela-S3	cervix
2	chr12:39092600-39153600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:39114200-39133600	Weak transcription	A549	lung
4	chr12:39115800-39164400	Weak transcription	Lung	lung
5	chr12:39116000-39154800	Weak transcription	Aorta	Aorta
6	chr12:39117000-39143200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:39117600-39126800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:39117600-39133600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:39118400-39143400	Weak transcription	Liver	Liver
10	chr12:39118400-39165600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:39118600-39133800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:39118600-39136000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:39123000-39131600	Weak transcription	GM12878-XiMat	blood
14	chr12:39123800-39142800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr12:39124200-39128800	Weak transcription	Monocytes-CD14+_RO01746	blood

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