Variant report

Variant	rs55828987
Chromosome Location	chr12:39056421-39056422
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10875979	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875991	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876086	0.87[AMR][1000 genomes]
rs1095575	0.91[EUR][1000 genomes]
rs11168505	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11168985	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169142	0.86[EUR][1000 genomes]
rs11169144	0.88[EUR][1000 genomes]
rs11169169	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169301	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169387	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11169508	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11169511	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11169547	0.87[AMR][1000 genomes]
rs11169666	0.81[AMR][1000 genomes]
rs11514111	0.83[AMR][1000 genomes]
rs11610376	0.87[AMR][1000 genomes]
rs11612004	0.81[AMR][1000 genomes]
rs12322306	0.88[EUR][1000 genomes]
rs1352122	0.89[EUR][1000 genomes]
rs1352123	0.87[EUR][1000 genomes]
rs1393537	0.81[AMR][1000 genomes]
rs1403523	0.87[EUR][1000 genomes]
rs1486345	0.89[EUR][1000 genomes]
rs1486357	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554550	0.81[AMR][1000 genomes]
rs1601579	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1684395	0.86[EUR][1000 genomes]
rs1684406	0.88[EUR][1000 genomes]
rs1684407	0.87[EUR][1000 genomes]
rs1684411	0.89[EUR][1000 genomes]
rs1684413	0.89[EUR][1000 genomes]
rs1684414	0.89[EUR][1000 genomes]
rs1684415	0.89[EUR][1000 genomes]
rs1684416	0.86[EUR][1000 genomes]
rs1719830	0.87[EUR][1000 genomes]
rs1719848	0.84[EUR][1000 genomes]
rs1719852	0.89[EUR][1000 genomes]
rs1719853	0.89[EUR][1000 genomes]
rs1719854	0.86[EUR][1000 genomes]
rs1719855	0.87[EUR][1000 genomes]
rs1719856	0.87[EUR][1000 genomes]
rs1719858	0.89[EUR][1000 genomes]
rs1843639	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2069211	0.88[EUR][1000 genomes]
rs34254519	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3886109	0.87[AMR][1000 genomes]
rs4768328	0.89[EUR][1000 genomes]
rs4768330	0.89[EUR][1000 genomes]
rs6580726	0.91[EUR][1000 genomes]
rs6580755	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7136593	0.89[EUR][1000 genomes]
rs7301104	0.87[AMR][1000 genomes]
rs7973992	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs826838	0.91[EUR][1000 genomes]
rs826851	0.89[EUR][1000 genomes]
rs826855	0.84[EUR][1000 genomes]
rs826856	0.89[EUR][1000 genomes]
rs826858	0.86[EUR][1000 genomes]
rs826870	0.89[EUR][1000 genomes]
rs826873	0.89[EUR][1000 genomes]
rs826874	0.81[EUR][1000 genomes]
rs826879	0.91[EUR][1000 genomes]
rs826886	0.91[EUR][1000 genomes]
rs826888	0.90[EUR][1000 genomes]
rs826889	0.90[EUR][1000 genomes]
rs826891	0.86[EUR][1000 genomes]
rs826892	0.86[EUR][1000 genomes]
rs844115	0.81[EUR][1000 genomes]
rs851934	0.86[EUR][1000 genomes]
rs860400	0.86[EUR][1000 genomes]
rs864324	0.82[EUR][1000 genomes]
rs864325	0.86[EUR][1000 genomes]
rs980571	0.88[EUR][1000 genomes]
rs980572	0.88[EUR][1000 genomes]
rs980573	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422488	chr12:38103874-39070734	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv1039821	chr12:38959645-39121578	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1053316	chr12:38959645-39122853	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1043831	chr12:38979065-39117868	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv541479	chr12:38979065-39117868	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv1045040	chr12:39038114-39084094	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55828987	ALG10B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39045400-39068000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:39046000-39085400	Weak transcription	Aorta	Aorta
3	chr12:39046800-39080400	Weak transcription	Spleen	Spleen
4	chr12:39051600-39080400	Weak transcription	Lung	lung
5	chr12:39051600-39080800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:39054600-39071000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:39055400-39058000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
8	chr12:39055800-39057000	Weak transcription	NHDF-Ad	bronchial
9	chr12:39055800-39100800	Weak transcription	NHEK	skin
10	chr12:39056000-39056800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:39056000-39061200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:39056000-39080200	Weak transcription	Ovary	ovary
13	chr12:39056000-39092200	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:39056000-39114800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:39056000-39168600	Weak transcription	Hela-S3	cervix
16	chr12:39056200-39056600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:39056200-39056800	Weak transcription	GM12878-XiMat	blood
18	chr12:39056200-39057800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:39056200-39057800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr12:39056200-39060200	Weak transcription	Liver	Liver
21	chr12:39056200-39078400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:39056200-39078400	Weak transcription	Adipose Nuclei	Adipose
23	chr12:39056200-39079000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:39056200-39080200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:39056400-39057400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:39056400-39058000	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr12:39056400-39058600	Enhancers	Primary hematopoietic stem cells	blood
28	chr12:39056400-39058600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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