Variant report

Variant	rs10875979
Chromosome Location	chr12:39095149-39095150
allele	A/G
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:79)

rs_ID	r²[population]
rs10506129	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10875991	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10876086	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1095575	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs11168505	0.84[ASN][1000 genomes]
rs11168985	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169031	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169142	0.89[EUR][1000 genomes]
rs11169144	0.91[EUR][1000 genomes]
rs11169169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169301	0.97[EUR][1000 genomes]
rs11169387	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs11169508	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs11169511	0.83[EUR][1000 genomes]
rs11169547	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11610376	0.81[EUR][1000 genomes]
rs11612004	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12322306	0.90[EUR][1000 genomes]
rs1352122	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs1352123	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs1403523	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs1486345	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs1486357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1554550	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1601579	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1684395	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs1684406	0.90[EUR][1000 genomes]
rs1684407	0.89[EUR][1000 genomes]
rs1684411	0.91[EUR][1000 genomes]
rs1684413	0.91[EUR][1000 genomes]
rs1684414	0.92[EUR][1000 genomes]
rs1684415	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs1684416	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs1719830	0.89[EUR][1000 genomes]
rs1719848	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs1719852	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs1719853	0.91[EUR][1000 genomes]
rs1719854	0.89[EUR][1000 genomes]
rs1719855	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs1719856	0.90[EUR][1000 genomes]
rs1719858	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs17523988	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1843639	0.82[EUR][1000 genomes]
rs2069211	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs34254519	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3886109	0.81[EUR][1000 genomes]
rs4768328	0.92[EUR][1000 genomes]
rs4768330	0.92[EUR][1000 genomes]
rs55828987	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6580726	0.93[EUR][1000 genomes]
rs6580755	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs7136593	0.91[EUR][1000 genomes]
rs7301104	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7973992	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs826838	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs826851	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs826855	0.87[EUR][1000 genomes]
rs826856	0.91[EUR][1000 genomes]
rs826858	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs826870	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs826873	0.91[EUR][1000 genomes]
rs826874	0.83[EUR][1000 genomes]
rs826876	0.96[CEU][hapmap]
rs826878	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs826879	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs826886	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs826888	0.93[EUR][1000 genomes]
rs826889	0.93[EUR][1000 genomes]
rs826891	0.88[EUR][1000 genomes]
rs826892	0.88[EUR][1000 genomes]
rs826893	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs844115	0.84[EUR][1000 genomes]
rs851934	0.89[EUR][1000 genomes]
rs860400	0.89[EUR][1000 genomes]
rs864324	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs864325	0.89[EUR][1000 genomes]
rs980571	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs980572	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs980573	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
4	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
5	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
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10875979	ALG10B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39055800-39100800	Weak transcription	NHEK	skin
2	chr12:39056000-39114800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:39056000-39168600	Weak transcription	Hela-S3	cervix
4	chr12:39066200-39114400	Weak transcription	Pancreas	Pancrea
5	chr12:39069400-39114600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr12:39074400-39098800	Weak transcription	Right Ventricle	heart
7	chr12:39079200-39114400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:39080600-39115600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:39080800-39095800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:39080800-39096200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:39080800-39097400	Weak transcription	Fetal Intestine Small	intestine
12	chr12:39080800-39098600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:39080800-39105000	Weak transcription	Adipose Nuclei	Adipose
14	chr12:39083400-39113200	Weak transcription	Left Ventricle	heart
15	chr12:39084200-39104800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:39086000-39114400	Weak transcription	Aorta	Aorta
17	chr12:39087200-39097400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:39087200-39113800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr12:39087800-39098400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:39089200-39113800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:39090800-39095800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr12:39092400-39095800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:39092600-39153600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:39092800-39095400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr12:39094000-39103800	Weak transcription	GM12878-XiMat	blood
26	chr12:39094200-39095200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:39094200-39096800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr12:39094600-39114600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:39094800-39097000	Weak transcription	Lung	lung
30	chr12:39095000-39114000	Weak transcription	Liver	Liver

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