Variant report

Variant	rs12425459
Chromosome Location	chr12:106852056-106852057
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:106845063..106848969-chr12:106849252..106852175,3	K562	blood:

Extended variants
information (count: 143 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10047654	0.88[ASN][1000 genomes]
rs10444532	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10507211	0.91[ASN][1000 genomes]
rs10746059	0.91[ASN][1000 genomes]
rs10746060	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778465	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778466	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778468	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778469	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778470	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778471	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778473	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778474	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778475	0.88[ASN][1000 genomes]
rs10778476	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778478	0.88[ASN][1000 genomes]
rs10778480	0.88[ASN][1000 genomes]
rs10778481	0.88[ASN][1000 genomes]
rs10778485	0.86[AMR][1000 genomes]
rs10861577	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10861578	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10861579	0.88[EUR][1000 genomes]
rs10861580	0.80[ASN][1000 genomes]
rs10861581	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861582	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861583	0.91[ASN][1000 genomes]
rs10861585	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861586	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861587	0.91[ASN][1000 genomes]
rs10861589	0.80[ASN][1000 genomes]
rs10861590	0.88[ASN][1000 genomes]
rs10861591	0.88[ASN][1000 genomes]
rs10861592	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861593	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861594	0.88[ASN][1000 genomes]
rs10861595	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861597	0.88[ASN][1000 genomes]
rs10861598	0.88[ASN][1000 genomes]
rs10861599	0.88[ASN][1000 genomes]
rs10861601	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861604	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861605	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861608	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861609	0.88[ASN][1000 genomes]
rs10861613	0.85[ASN][1000 genomes]
rs10861614	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11112945	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11112949	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11112951	0.91[ASN][1000 genomes]
rs11112952	0.91[ASN][1000 genomes]
rs11112953	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11112957	0.80[ASN][1000 genomes]
rs11112961	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11112971	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112979	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112980	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112986	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11112990	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112991	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112992	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112993	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11112995	0.88[ASN][1000 genomes]
rs11113003	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11113004	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11113009	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11609315	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611176	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611252	0.88[ASN][1000 genomes]
rs11611815	0.80[EUR][1000 genomes]
rs11835357	0.88[ASN][1000 genomes]
rs11835362	1.00[ASN][1000 genomes]
rs12298876	0.88[ASN][1000 genomes]
rs12305705	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12309708	0.88[ASN][1000 genomes]
rs12309758	0.88[ASN][1000 genomes]
rs12312915	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12423068	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424952	0.84[ASN][1000 genomes]
rs17038414	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17218490	0.84[ASN][1000 genomes]
rs17285274	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2141774	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2288268	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2374606	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2374610	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28475238	0.85[AMR][1000 genomes]
rs2900499	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2900500	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34955444	0.91[ASN][1000 genomes]
rs3851631	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851632	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3851633	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4509864	0.84[ASN][1000 genomes]
rs4522273	0.86[AMR][1000 genomes]
rs4625578	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55678155	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55689816	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60635749	0.88[ASN][1000 genomes]
rs61941917	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61941918	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61941920	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61941921	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61941922	0.88[ASN][1000 genomes]
rs61941943	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61941944	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943670	0.88[EUR][1000 genomes]
rs61943672	0.91[ASN][1000 genomes]
rs61943690	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943693	0.96[ASN][1000 genomes]
rs61943694	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6539268	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6539269	0.88[ASN][1000 genomes]
rs6539270	0.88[ASN][1000 genomes]
rs6539271	0.88[ASN][1000 genomes]
rs67911933	0.80[ASN][1000 genomes]
rs67966244	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132744	0.86[EUR][1000 genomes]
rs7134615	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7134881	0.95[ASN][1000 genomes]
rs7135054	0.91[ASN][1000 genomes]
rs7136098	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7137445	0.88[ASN][1000 genomes]
rs7139139	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7139249	0.88[ASN][1000 genomes]
rs7296090	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7297873	0.88[ASN][1000 genomes]
rs7298062	0.82[EUR][1000 genomes]
rs7303873	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7306277	0.88[ASN][1000 genomes]
rs7306326	0.88[ASN][1000 genomes]
rs7307711	0.88[AMR][1000 genomes]
rs7308541	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7309020	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7310703	0.91[ASN][1000 genomes]
rs7311957	0.80[ASN][1000 genomes]
rs7315549	0.88[ASN][1000 genomes]
rs7963213	0.88[ASN][1000 genomes]
rs7965520	0.88[ASN][1000 genomes]
rs7969743	0.88[ASN][1000 genomes]
rs7971581	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7976305	0.88[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
rs12425459	POLR3B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106787600-106856600	Weak transcription	GM12878-XiMat	blood
2	chr12:106787800-106852400	Weak transcription	Gastric	stomach
3	chr12:106787800-106852800	Weak transcription	Pancreas	Pancrea
4	chr12:106802400-106854000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr12:106812000-106855000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:106813000-106864800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:106813200-106852800	Weak transcription	HMEC	breast
8	chr12:106813200-106855800	Weak transcription	NHDF-Ad	bronchial
9	chr12:106813200-106864800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:106814400-106855800	Weak transcription	Stomach Mucosa	stomach
11	chr12:106819400-106855600	Weak transcription	Right Ventricle	heart
12	chr12:106822000-106852400	Weak transcription	Brain Angular Gyrus	brain
13	chr12:106822000-106853400	Weak transcription	Fetal Brain Female	brain
14	chr12:106823200-106858000	Weak transcription	Psoas Muscle	Psoas
15	chr12:106824800-106866400	Weak transcription	NHLF	lung
16	chr12:106827200-106853000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr12:106827200-106853200	Weak transcription	Fetal Heart	heart
18	chr12:106828600-106905800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:106828800-106852400	Weak transcription	Fetal Thymus	thymus
20	chr12:106828800-106855800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:106828800-106856400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:106829000-106867200	Weak transcription	Colon Smooth Muscle	Colon
23	chr12:106830400-106864600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr12:106830400-106865800	Weak transcription	K562	blood
25	chr12:106830600-106852400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr12:106830600-106853000	Weak transcription	HepG2	liver
27	chr12:106831200-106852200	Weak transcription	NHEK	skin
28	chr12:106831200-106856200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:106831400-106855200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr12:106831600-106856400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr12:106831600-106856400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr12:106833000-106864400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:106834400-106852200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:106834400-106853000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr12:106834600-106852200	Weak transcription	Esophagus	oesophagus
36	chr12:106835400-106852200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr12:106839400-106852600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:106840000-106852800	Weak transcription	Brain Hippocampus Middle	brain
39	chr12:106840000-106864600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:106840800-106853000	Weak transcription	Brain Substantia Nigra	brain
41	chr12:106840800-106853200	Weak transcription	Brain Anterior Caudate	brain
42	chr12:106840800-106855600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:106841400-106852800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr12:106841600-106852200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr12:106841600-106852400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr12:106841600-106853200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr12:106841600-106853400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr12:106841600-106853800	Weak transcription	Brain Germinal Matrix	brain
49	chr12:106841800-106853400	Weak transcription	NH-A	brain
50	chr12:106841800-106865000	Weak transcription	A549	lung

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