Variant report

Variant	rs688100
Chromosome Location	chr1:169968152-169968153
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10800494	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10800495	1.00[JPT][hapmap]
rs10919284	1.00[JPT][hapmap]
rs11585754	0.88[JPT][hapmap]
rs11803298	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11807405	0.81[ASN][1000 genomes]
rs12123693	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12124607	0.86[JPT][hapmap]
rs12126204	1.00[JPT][hapmap]
rs12137754	0.86[JPT][hapmap]
rs12144417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12146137	1.00[JPT][hapmap]
rs12750962	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13374766	0.88[JPT][hapmap]
rs1360293	1.00[JPT][hapmap]
rs2273457	0.92[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs34866861	0.81[ASN][1000 genomes]
rs4656729	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4656737	0.88[JPT][hapmap]
rs6427233	1.00[JPT][hapmap]
rs6657512	1.00[JPT][hapmap]
rs6670191	1.00[JPT][hapmap]
rs6674620	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6678382	0.81[ASN][1000 genomes]
rs7514634	0.85[JPT][hapmap]
rs7521273	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1012520	chr1:169899427-169969444	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1010370	chr1:169917450-169980951	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs688100	METTL18	cis	Thyroid	GTEx
rs688100	C1orf156	cis	lymphoblastoid	seeQTL
rs688100	KIFAP3	cis	cerebellum	SCAN
rs688100	GPA33	cis	cerebellum	SCAN
rs688100	METTL18	cis	Esophagus Muscularis	GTEx
rs688100	METTL18	cis	Artery Tibial	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169904000-170010400	Weak transcription	Aorta	Aorta
2	chr1:169911800-169968400	Weak transcription	Psoas Muscle	Psoas
3	chr1:169912000-169968600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:169913800-169968400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:169914000-169968400	Weak transcription	Ovary	ovary
6	chr1:169914800-169984000	Weak transcription	Left Ventricle	heart
7	chr1:169914800-169984800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr1:169914800-169988800	Weak transcription	Fetal Intestine Small	intestine
9	chr1:169921600-169968400	Weak transcription	Fetal Brain Male	brain
10	chr1:169922000-169984000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:169922200-169968400	Weak transcription	Brain Angular Gyrus	brain
12	chr1:169922400-169996400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:169930400-169968400	Weak transcription	Small Intestine	intestine
14	chr1:169935600-169968400	Weak transcription	Fetal Kidney	kidney
15	chr1:169938000-169968400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:169939000-169968400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:169944800-169989600	Weak transcription	Thymus	Thymus
18	chr1:169945400-169968400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:169945800-169975000	Weak transcription	GM12878-XiMat	blood
20	chr1:169946400-169968400	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:169948800-169968200	Weak transcription	HSMMtube	muscle
22	chr1:169951600-170011800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr1:169951800-169975000	Weak transcription	Dnd41	blood
24	chr1:169951800-169975200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:169951800-169984800	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr1:169952000-169983200	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr1:169952000-169984600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:169952000-169985200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:169952000-170018000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:169952200-169983000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:169952400-169983000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:169952400-169984600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:169952400-170043000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:169952600-169975400	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:169952600-169984800	Weak transcription	Fetal Intestine Large	intestine
36	chr1:169954600-169968200	Weak transcription	Colon Smooth Muscle	Colon
37	chr1:169954800-169968400	Weak transcription	Adipose Nuclei	Adipose
38	chr1:169955000-169984800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:169955600-169984800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:169956800-169997400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:169960800-169970800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:169960800-169975000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:169966400-169968400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:169966400-169968600	Weak transcription	Primary T cells from cord blood	blood
45	chr1:169966600-169984600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr1:169966800-169984600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr1:169966800-169984800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:169967200-169971400	Enhancers	NHDF-Ad	bronchial
49	chr1:169967200-169971600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:169967400-169968400	Enhancers	NHEK	skin

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