Variant report

Variant	rs28419113
Chromosome Location	chr17:18202409-18202410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11868259	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11870126	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12936652	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12936769	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12937300	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12939259	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12939357	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12939757	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12945597	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12946058	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12949078	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12949983	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12952556	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12952667	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1563631	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1563633	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979276	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1979277	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2230154	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273028	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2273030	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386456	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2386457	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2386458	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605142	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2746023	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2746024	0.97[ASN][1000 genomes]
rs3764405	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3783	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3794771	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794772	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3829583	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4632181	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924842	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924843	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4924845	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924847	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925160	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925162	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925163	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925167	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925169	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925171	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925172	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58215032	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6502643	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502644	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502646	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6502649	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66903818	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207123	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215839	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7222684	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7223122	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8068602	0.83[EUR][1000 genomes]
rs8068854	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8070633	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8071231	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074444	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8080966	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs921865	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs921866	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs921986	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs941451	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9898631	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription 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 miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
6	nsv907773	chr17:18099962-18206234	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv907774	chr17:18103907-18206234	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv907775	chr17:18108496-18206234	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv833386	chr17:18170261-18332726	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
10	nsv1057081	chr17:18171516-18256347	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv543247	chr17:18171516-18256347	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	nsv1062368	chr17:18180747-18259234	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv833387	chr17:18200081-18378155	Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
14	esv1806346	chr17:18200081-18446384	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
15	esv1812661	chr17:18200081-18446384	Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
16	nsv428333	chr17:18200081-18446384	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
17	nsv427992	chr17:18200081-19192047	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs28419113	SHMT1	cis	multi-tissue	Pritchard
rs28419113	SHMT1	cis	Nerve Tibial	GTEx
rs28419113	SHMT1	cis	Muscle Skeletal	GTEx
rs28419113	SHMT1	cis	Artery Tibial	GTEx
rs28419113	LGALS9C	cis	Whole Blood	GTEx
rs28419113	ALKBH5	cis	Esophagus Muscularis	GTEx
rs28419113	LLGL1	cis	Esophagus Mucosa	GTEx
rs28419113	RP11-258F1.1	cis	Esophagus Muscularis	GTEx
rs28419113	SHMT1	cis	Esophagus Muscularis	GTEx
rs28419113	SHMT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18172200-18217400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:18173000-18213800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:18183600-18207000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr17:18184800-18217000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr17:18189000-18202800	Weak transcription	Stomach Mucosa	stomach
6	chr17:18193800-18204000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:18194400-18202800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr17:18194600-18202600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr17:18194600-18202600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr17:18194600-18208000	Weak transcription	Fetal Brain Male	brain
11	chr17:18194600-18215600	Weak transcription	Fetal Heart	heart
12	chr17:18195800-18209600	Weak transcription	Psoas Muscle	Psoas
13	chr17:18196000-18202600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr17:18196000-18204200	Weak transcription	Small Intestine	intestine
15	chr17:18196200-18202600	Weak transcription	Colon Smooth Muscle	Colon
16	chr17:18196400-18202600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr17:18196400-18202600	Weak transcription	Pancreas	Pancrea
18	chr17:18196600-18202600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr17:18196600-18202600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr17:18196600-18202600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr17:18196600-18202600	Weak transcription	Gastric	stomach
22	chr17:18196600-18202600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr17:18196600-18202800	Weak transcription	Colonic Mucosa	Colon
24	chr17:18196800-18202600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr17:18196800-18203200	Weak transcription	NHDF-Ad	bronchial
26	chr17:18196800-18217000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr17:18197400-18202600	Weak transcription	Brain Substantia Nigra	brain
28	chr17:18198200-18202600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr17:18198200-18202600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr17:18198200-18202600	Weak transcription	Right Ventricle	heart
31	chr17:18198200-18202600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr17:18198200-18202800	Weak transcription	NHEK	skin
33	chr17:18198400-18202600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr17:18198400-18202600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr17:18198400-18202600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr17:18198400-18202600	Weak transcription	Brain Angular Gyrus	brain
37	chr17:18198400-18202600	Weak transcription	Brain Hippocampus Middle	brain
38	chr17:18198400-18202600	Weak transcription	Fetal Kidney	kidney
39	chr17:18198400-18202600	Weak transcription	Fetal Lung	lung
40	chr17:18198400-18202600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr17:18198400-18202600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr17:18198400-18202600	Weak transcription	GM12878-XiMat	blood
43	chr17:18198400-18202600	Weak transcription	HepG2	liver
44	chr17:18198400-18202600	Weak transcription	HMEC	breast
45	chr17:18198400-18202600	Weak transcription	HSMM	muscle
46	chr17:18198400-18202600	Weak transcription	HSMMtube	muscle
47	chr17:18198400-18202800	Weak transcription	NHLF	lung
48	chr17:18198600-18202600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr17:18198600-18202600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr17:18198600-18202600	Weak transcription	Esophagus	oesophagus

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