Variant report

Variant	rs10778483
Chromosome Location	chr12:106906914-106906915
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10778484	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861600	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10861607	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10861615	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861616	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11112983	0.81[EUR][1000 genomes]
rs11113012	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11113014	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11113015	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11113016	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11113020	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11113023	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11113025	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12231768	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17038484	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1882413	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2243506	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs2245062	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs2246353	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2249162	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2249773	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs2250262	0.86[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes]
rs2252685	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2253054	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs2288266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288269	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2374609	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34619628	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3851635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3902141	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs741624	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3435035	chr12:106765277-107015325	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv832510	chr12:106787730-106951140	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10778483	POLR3B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106886200-106916400	Weak transcription	A549	lung
2	chr12:106887600-106907800	Weak transcription	Small Intestine	intestine
3	chr12:106892000-106907800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr12:106894400-106916400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:106894600-106913200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:106896400-106907200	Weak transcription	Esophagus	oesophagus
7	chr12:106896400-106908400	Weak transcription	NHLF	lung
8	chr12:106896400-106916800	Weak transcription	Fetal Intestine Small	intestine
9	chr12:106898200-106907600	Weak transcription	K562	blood
10	chr12:106898600-106916000	Weak transcription	HepG2	liver
11	chr12:106898800-106913200	Weak transcription	Fetal Lung	lung
12	chr12:106899000-106907000	Weak transcription	Gastric	stomach
13	chr12:106899200-106907000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:106899600-106911000	Weak transcription	Brain Germinal Matrix	brain
15	chr12:106900800-106907000	Weak transcription	Lung	lung
16	chr12:106900800-106908000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:106900800-106908600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:106900800-106908800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:106901000-106913200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr12:106901600-106908000	Weak transcription	Hela-S3	cervix
21	chr12:106901600-106909200	Weak transcription	Fetal Kidney	kidney
22	chr12:106903800-106907000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:106903800-106907800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:106903800-106908200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:106904000-106907000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:106904000-106908800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:106904200-106908000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:106904400-106907200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:106904600-106908600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr12:106904600-106908800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:106904800-106907000	Weak transcription	Right Ventricle	heart
32	chr12:106904800-106912800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:106905200-106907600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:106905400-106908400	Weak transcription	Pancreas	Pancrea
35	chr12:106905600-106907200	Weak transcription	Placenta	Placenta
36	chr12:106905600-106909200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:106905600-106913400	Weak transcription	Fetal Muscle Leg	muscle
38	chr12:106905800-106913000	Weak transcription	Fetal Stomach	stomach
39	chr12:106906800-106907200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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