Variant report

Variant	rs58215032
Chromosome Location	chr17:18201517-18201518
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:18199993..18202110-chr17:18203677..18206033,2	K562	blood:

Variant related genes	Relation type
ENSG00000177302	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11868259	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11870126	0.88[EUR][1000 genomes]
rs12936652	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12936769	0.82[EUR][1000 genomes]
rs12937300	0.90[EUR][1000 genomes]
rs12939259	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12939357	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12939757	0.89[EUR][1000 genomes]
rs12945597	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12946058	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12949078	0.90[EUR][1000 genomes]
rs12949983	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12952556	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12952667	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1563631	0.91[EUR][1000 genomes]
rs1563633	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1979276	0.87[EUR][1000 genomes]
rs1979277	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2230154	0.89[EUR][1000 genomes]
rs2273028	0.84[EUR][1000 genomes]
rs2273030	0.88[EUR][1000 genomes]
rs2386456	0.89[EUR][1000 genomes]
rs2386457	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2386458	0.86[EUR][1000 genomes]
rs2605142	0.81[EUR][1000 genomes]
rs2746023	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28419113	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3764405	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3783	0.91[EUR][1000 genomes]
rs3794771	0.90[EUR][1000 genomes]
rs3794772	0.83[EUR][1000 genomes]
rs3829583	0.88[EUR][1000 genomes]
rs4632181	0.92[EUR][1000 genomes]
rs4924842	0.82[EUR][1000 genomes]
rs4924843	0.85[EUR][1000 genomes]
rs4924845	0.87[EUR][1000 genomes]
rs4924847	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4925160	0.85[EUR][1000 genomes]
rs4925162	0.85[EUR][1000 genomes]
rs4925163	0.83[EUR][1000 genomes]
rs4925167	0.90[EUR][1000 genomes]
rs4925169	0.87[EUR][1000 genomes]
rs4925171	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4925172	0.87[EUR][1000 genomes]
rs6502643	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6502644	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6502646	0.91[EUR][1000 genomes]
rs6502649	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66903818	0.90[EUR][1000 genomes]
rs7207123	0.88[EUR][1000 genomes]
rs7215839	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7222684	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7223122	0.85[EUR][1000 genomes]
rs8068854	0.88[EUR][1000 genomes]
rs8070633	0.83[EUR][1000 genomes]
rs8071231	0.85[EUR][1000 genomes]
rs8074444	0.87[EUR][1000 genomes]
rs8080966	0.92[EUR][1000 genomes]
rs921865	0.87[EUR][1000 genomes]
rs921866	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs921986	0.87[EUR][1000 genomes]
rs941451	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9898631	0.86[EUR][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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs58215032	SHMT1	cis	Nerve Tibial	GTEx
rs58215032	SHMT1	cis	Artery Tibial	GTEx
rs58215032	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs58215032	SHMT1	cis	Esophagus Muscularis	GTEx
rs58215032	ALKBH5	cis	Esophagus Muscularis	GTEx
rs58215032	RP11-258F1.1	cis	Esophagus Muscularis	GTEx
rs58215032	LGALS9C	cis	Whole Blood	GTEx
rs58215032	LLGL1	cis	Esophagus Mucosa	GTEx
rs58215032	SHMT1	cis	Muscle Skeletal	GTEx

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	chr17:18196600-18202400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr17:18196600-18202400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr17:18196600-18202400	Weak transcription	HUVEC	blood vessel
21	chr17:18196600-18202600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr17:18196600-18202600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr17:18196600-18202600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr17:18196600-18202600	Weak transcription	Gastric	stomach
25	chr17:18196600-18202600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr17:18196600-18202800	Weak transcription	Colonic Mucosa	Colon
27	chr17:18196800-18202600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr17:18196800-18203200	Weak transcription	NHDF-Ad	bronchial
29	chr17:18196800-18217000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr17:18197000-18202400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr17:18197000-18202400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr17:18197400-18202400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr17:18197400-18202400	Weak transcription	Left Ventricle	heart
34	chr17:18197400-18202600	Weak transcription	Brain Substantia Nigra	brain
35	chr17:18198200-18202400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr17:18198200-18202400	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr17:18198200-18202400	Weak transcription	Brain Germinal Matrix	brain
38	chr17:18198200-18202400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr17:18198200-18202400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr17:18198200-18202600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr17:18198200-18202600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr17:18198200-18202600	Weak transcription	Right Ventricle	heart
43	chr17:18198200-18202600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr17:18198200-18202800	Weak transcription	NHEK	skin
45	chr17:18198400-18202400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr17:18198400-18202400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr17:18198400-18202400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr17:18198400-18202400	Weak transcription	Adipose Nuclei	Adipose
49	chr17:18198400-18202400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr17:18198400-18202400	Weak transcription	Fetal Thymus	thymus

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