Variant report

Variant	rs12750962
Chromosome Location	chr1:170004508-170004509
allele	A/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	TCF7L2	chr1:170004263-170004765	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
KIFAP3	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10800494	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10800495	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10919270	0.80[CHB][hapmap]
rs10919271	0.80[CHB][hapmap]
rs10919284	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10919285	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10919289	0.93[ASN][1000 genomes]
rs10919291	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10919292	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11585754	0.86[JPT][hapmap]
rs11803298	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11804170	0.80[CHB][hapmap]
rs11807267	0.84[ASN][1000 genomes]
rs11807405	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12116880	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12123693	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12124607	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.84[ASN][1000 genomes]
rs12126204	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12131429	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12137754	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12143011	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12144417	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12146137	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12754717	0.84[ASN][1000 genomes]
rs13374766	0.86[JPT][hapmap]
rs1360293	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs17349726	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1983986	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2273457	0.85[JPT][hapmap]
rs28854261	0.98[ASN][1000 genomes]
rs34866861	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs35688996	0.84[YRI][hapmap]
rs4656729	1.00[JPT][hapmap]
rs4656737	0.86[JPT][hapmap]
rs6427233	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6657512	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6658442	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6670191	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6674620	1.00[JPT][hapmap]
rs6678382	0.95[ASN][1000 genomes]
rs6694135	0.98[ASN][1000 genomes]
rs688100	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7514634	0.90[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs7521273	0.82[JPT][hapmap];0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7555871	0.92[AFR][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	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12750962	METTL18	cis	Thyroid	GTEx
rs12750962	METTL18	cis	Esophagus Muscularis	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169904000-170010400	Weak transcription	Aorta	Aorta
2	chr1:169951600-170011800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:169952000-170018000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:169952400-170043000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:169967600-170013000	Weak transcription	Fetal Heart	heart
6	chr1:169968800-170010800	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:169968800-170020200	Weak transcription	Brain Angular Gyrus	brain
8	chr1:169969000-170012600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:169969600-170017800	Weak transcription	Esophagus	oesophagus
10	chr1:169979400-170018000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:169979800-170015200	Weak transcription	HMEC	breast
12	chr1:169980000-170006600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:169981600-170013400	Weak transcription	Lung	lung
14	chr1:169982400-170020600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:169983000-170017200	Weak transcription	HSMMtube	muscle
16	chr1:169983800-170017600	Weak transcription	Spleen	Spleen
17	chr1:169984600-170020800	Weak transcription	Gastric	stomach
18	chr1:169984800-170027600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr1:169985000-170010800	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:169985000-170012800	Weak transcription	Brain Anterior Caudate	brain
21	chr1:169985200-170020400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:169985800-170010800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:169985800-170010800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:169986200-170006600	Weak transcription	Ovary	ovary
25	chr1:169986200-170010600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:169986400-170013600	Weak transcription	Left Ventricle	heart
27	chr1:169986400-170019800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:169988000-170017600	Weak transcription	Fetal Lung	lung
29	chr1:169989200-170006400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr1:169989600-170019800	Weak transcription	Right Ventricle	heart
31	chr1:169989800-170013400	Weak transcription	Psoas Muscle	Psoas
32	chr1:169990400-170017200	Weak transcription	Fetal Kidney	kidney
33	chr1:169993600-170010800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:169993600-170021400	Weak transcription	Fetal Brain Male	brain
35	chr1:169995400-170017800	Weak transcription	Pancreas	Pancrea
36	chr1:169995800-170006200	Weak transcription	Liver	Liver
37	chr1:169996800-170010000	Weak transcription	Brain Germinal Matrix	brain
38	chr1:169997200-170006200	Weak transcription	Adipose Nuclei	Adipose
39	chr1:169997200-170006200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:169997200-170010600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr1:169997200-170010800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr1:169997200-170012400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:169997400-170012000	Weak transcription	Primary B cells from cord blood	blood
44	chr1:169997800-170010000	Weak transcription	Fetal Stomach	stomach
45	chr1:169997800-170010600	Weak transcription	Fetal Thymus	thymus
46	chr1:169997800-170017600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:169997800-170018600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:169998000-170006600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:169998000-170010600	Weak transcription	Fetal Muscle Leg	muscle
50	chr1:169998000-170011400	Weak transcription	Primary hematopoietic stem cells	blood

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