Variant report

Variant	rs56021431
Chromosome Location	chr17:18096391-18096392
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11869205	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870766	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11871970	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12150618	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12451754	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12936694	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12939469	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12946842	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1378601	0.85[ASN][1000 genomes]
rs1378602	0.85[ASN][1000 genomes]
rs2360234	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2605132	0.90[EUR][1000 genomes]
rs28641923	0.96[ASN][1000 genomes]
rs2925137	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925138	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4603612	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924839	0.90[ASN][1000 genomes]
rs4924840	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924841	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4925149	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925150	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs712270	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs712272	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs712273	0.90[ASN][1000 genomes]
rs712275	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7212808	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8071834	0.92[ASN][1000 genomes]
rs854771	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs854795	0.90[ASN][1000 genomes]
rs854797	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs854798	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs854799	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs854801	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854804	0.90[ASN][1000 genomes]
rs854805	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs854806	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs854807	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs860567	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs860568	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs861278	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv907770	chr17:18003845-18098018	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv907771	chr17:18013560-18098018	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv907772	chr17:18030524-18098018	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv510702	chr17:18037676-18116801	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs56021431	SHMT1	cis	Artery Tibial	GTEx
rs56021431	LGALS9C	cis	Whole Blood	GTEx
rs56021431	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs56021431	SHMT1	cis	Muscle Skeletal	GTEx
rs56021431	LLGL1	cis	Esophagus Mucosa	GTEx
rs56021431	SHMT1	cis	Esophagus Muscularis	GTEx
rs56021431	RP11-258F1.1	cis	Esophagus Muscularis	GTEx
rs56021431	ALKBH5	cis	Esophagus Muscularis	GTEx
rs56021431	ALKBH5	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18090200-18103400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:18090800-18098200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:18090800-18098400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr17:18090800-18104000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr17:18091200-18097000	Genic enhancers	Primary T cells fromperipheralblood	blood
6	chr17:18091200-18104600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr17:18091400-18097000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr17:18091400-18098800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr17:18091400-18114000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:18091600-18097800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr17:18091800-18098000	Weak transcription	Primary B cells from cord blood	blood
12	chr17:18091800-18098200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr17:18091800-18114400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr17:18092000-18098000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr17:18092000-18104000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr17:18092200-18098000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr17:18092200-18098200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr17:18092800-18096400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr17:18093000-18098800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr17:18093200-18096400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr17:18093400-18097800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr17:18093400-18097800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr17:18093400-18098000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr17:18094200-18096400	Weak transcription	Hela-S3	cervix
25	chr17:18094200-18098200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr17:18094200-18114600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr17:18094400-18097800	Weak transcription	HMEC	breast
28	chr17:18094400-18098200	Weak transcription	Fetal Heart	heart
29	chr17:18094400-18114600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr17:18094600-18114600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr17:18094800-18096800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr17:18094800-18097800	Weak transcription	NHLF	lung
33	chr17:18094800-18098200	Weak transcription	Fetal Lung	lung
34	chr17:18094800-18098200	Weak transcription	HSMM	muscle
35	chr17:18094800-18098600	Weak transcription	HSMMtube	muscle
36	chr17:18094800-18098600	Weak transcription	NH-A	brain
37	chr17:18094800-18101800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr17:18094800-18103400	Strong transcription	Fetal Intestine Large	intestine
39	chr17:18095000-18096600	Strong transcription	Primary B cells from peripheral blood	blood
40	chr17:18095000-18096800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr17:18095000-18097000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr17:18095000-18097000	Weak transcription	Gastric	stomach
43	chr17:18095000-18097000	Weak transcription	A549	lung
44	chr17:18095000-18097000	Weak transcription	K562	blood
45	chr17:18095000-18097400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
46	chr17:18095000-18097800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr17:18095000-18097800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr17:18095000-18097800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr17:18095000-18097800	Weak transcription	Fetal Brain Female	brain
50	chr17:18095000-18098200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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