Variant report

Variant	rs12305170
Chromosome Location	chr12:51345265-51345266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:51344899-51345333	HL-60	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000271596	TF binding region
HIGD1C	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1079521	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169627	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169632	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12304878	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304921	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306808	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12310511	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12315928	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316856	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12317171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12318464	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12582592	0.82[JPT][hapmap]
rs17122760	0.88[CEU][hapmap];0.95[CHB][hapmap]
rs17125088	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17125116	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17125286	0.95[CHB][hapmap]
rs17125346	0.95[CHB][hapmap]
rs17125375	0.81[JPT][hapmap]
rs17125401	0.82[JPT][hapmap]
rs224446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs224454	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs224568	1.00[CEU][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs224587	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2269684	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2269685	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2269686	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs453313	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4768869	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4768941	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768942	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768943	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768944	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768945	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55871024	0.87[AMR][1000 genomes]
rs56087503	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56303785	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56353532	0.87[AMR][1000 genomes]
rs56402416	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58999537	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59546367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61005916	0.87[AMR][1000 genomes]
rs61577980	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66518563	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66744607	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67106267	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67420027	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67646958	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67654320	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67669227	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73090619	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73090629	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73090630	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73090631	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73090647	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73090649	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73090660	0.87[AMR][1000 genomes]
rs73090661	0.87[AMR][1000 genomes]
rs73090666	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73092531	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73092534	0.87[AMR][1000 genomes]
rs73092537	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73295896	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73310004	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73310020	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7397054	0.81[EUR][1000 genomes]
rs7397068	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7973904	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12305170	KRT1	cis	parietal	SCAN
rs12305170	TFCP2	Cis_1M	lymphoblastoid	RTeQTL
rs12305170	TFCP2	cis	lymphoblastoid	seeQTL
rs12305170	C12orf54	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51319400-51346200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:51323000-51377200	Weak transcription	Aorta	Aorta
3	chr12:51328800-51378000	Weak transcription	Brain Substantia Nigra	brain
4	chr12:51329600-51373600	Weak transcription	Left Ventricle	heart
5	chr12:51331400-51378400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:51331600-51373800	Weak transcription	Pancreas	Pancrea
7	chr12:51331800-51353800	Weak transcription	Primary T cells from cord blood	blood
8	chr12:51331800-51382000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:51331800-51382000	Weak transcription	Ovary	ovary
10	chr12:51332000-51346400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:51332400-51346200	Weak transcription	Fetal Intestine Small	intestine
12	chr12:51332400-51346200	Weak transcription	Fetal Muscle Leg	muscle
13	chr12:51332400-51346200	Weak transcription	Fetal Stomach	stomach
14	chr12:51332600-51346400	Weak transcription	Brain Angular Gyrus	brain
15	chr12:51332600-51354400	Weak transcription	Thymus	Thymus
16	chr12:51332600-51365000	Weak transcription	Fetal Brain Female	brain
17	chr12:51340000-51361800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:51341400-51348600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:51341600-51378200	Weak transcription	Right Ventricle	heart
20	chr12:51341800-51372600	Weak transcription	Osteobl	bone
21	chr12:51341800-51383200	Weak transcription	Fetal Brain Male	brain
22	chr12:51342200-51361200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr12:51342400-51360000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:51342400-51373200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:51342800-51346600	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr12:51342800-51378400	Weak transcription	NHLF	lung
27	chr12:51343000-51355400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr12:51343000-51366200	Weak transcription	Brain Germinal Matrix	brain
29	chr12:51343200-51346200	Weak transcription	Brain Anterior Caudate	brain
30	chr12:51343200-51346400	Weak transcription	Brain Hippocampus Middle	brain
31	chr12:51343200-51361600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:51343400-51355200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:51343600-51366200	Weak transcription	Gastric	stomach
34	chr12:51344000-51346200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr12:51344000-51346400	Weak transcription	Lung	lung
36	chr12:51344000-51361400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr12:51344000-51382000	Weak transcription	Esophagus	oesophagus
38	chr12:51344600-51381600	Weak transcription	Spleen	Spleen
39	chr12:51344800-51345400	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr12:51344800-51345600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:51344800-51345600	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr12:51345000-51361200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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