Variant report

Variant	rs7312879
Chromosome Location	chr12:39150752-39150753
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10161183	0.84[AFR][1000 genomes]
rs10506124	0.83[ASN][1000 genomes]
rs10506125	0.81[EUR][1000 genomes]
rs10506126	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10506127	0.85[EUR][1000 genomes]
rs10783329	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10783330	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783333	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875953	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875954	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10876005	0.81[EUR][1000 genomes]
rs10876008	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169006	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169054	0.85[ASN][1000 genomes]
rs11169100	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169189	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169222	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169258	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169482	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11169518	0.80[EUR][1000 genomes]
rs11169519	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12229104	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12231313	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12300353	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12314639	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12424190	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12818797	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12822023	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12831609	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1352121	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1386018	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1875609	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34311455	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35254764	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3759139	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4616077	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61937754	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7309400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7315271	0.86[AMR][1000 genomes]
rs7316392	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7960616	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7979541	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9325144	0.83[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
rs7312879	ALG10B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 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	chr12:39115800-39164400	Weak transcription	Lung	lung
4	chr12:39116000-39154800	Weak transcription	Aorta	Aorta
5	chr12:39118400-39165600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:39135800-39159000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:39139000-39153600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:39140600-39155000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:39141000-39155800	Weak transcription	Ovary	ovary
10	chr12:39141800-39153600	Weak transcription	Adipose Nuclei	Adipose
11	chr12:39142400-39154200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:39143800-39153200	Weak transcription	Liver	Liver
13	chr12:39144200-39163400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:39144200-39173800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:39144400-39152400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr12:39144400-39153600	Weak transcription	Left Ventricle	heart
17	chr12:39144600-39156200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:39145000-39153200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:39146000-39153600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:39146400-39165400	Weak transcription	GM12878-XiMat	blood
21	chr12:39149200-39150800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr12:39149400-39154800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr12:39149800-39155400	Weak transcription	Right Ventricle	heart
24	chr12:39150400-39154800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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