Variant report

Variant	rs7212808
Chromosome Location	chr17:18096846-18096847
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11869205	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11870766	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11871970	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12150618	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12451754	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12936694	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12939469	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12946842	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1378601	0.82[ASN][1000 genomes]
rs1378602	0.82[ASN][1000 genomes]
rs2360234	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2605132	0.88[EUR][1000 genomes]
rs2605137	0.81[AMR][1000 genomes]
rs2746027	0.82[AMR][1000 genomes]
rs28641923	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2925137	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2925138	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4603612	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4924839	0.86[ASN][1000 genomes]
rs4924840	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924841	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925149	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4925150	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56021431	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs712270	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs712272	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs712273	0.86[ASN][1000 genomes]
rs712275	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8071834	0.88[ASN][1000 genomes]
rs854771	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs854795	0.86[ASN][1000 genomes]
rs854797	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs854798	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs854799	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs854801	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs854804	0.86[ASN][1000 genomes]
rs854805	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs854806	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs854807	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs860567	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs860568	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs861278	0.88[AMR][1000 genomes];0.92[EUR][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7212808	RP11-258F1.1	cis	Esophagus Muscularis	GTEx
rs7212808	SHMT1	cis	Artery Tibial	GTEx
rs7212808	LGALS9C	cis	Whole Blood	GTEx
rs7212808	SHMT1	cis	Muscle Skeletal	GTEx
rs7212808	LLGL1	cis	Esophagus Mucosa	GTEx
rs7212808	SHMT1	cis	Esophagus Muscularis	GTEx
rs7212808	ALKBH5	cis	Esophagus Muscularis	GTEx
rs7212808	SHMT1	Cis_1M	lymphoblastoid	RTeQTL

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	chr17:18093000-18098800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr17:18093400-18097800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr17:18093400-18097800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr17:18093400-18098000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr17:18094200-18098200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr17:18094200-18114600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr17:18094400-18097800	Weak transcription	HMEC	breast
25	chr17:18094400-18098200	Weak transcription	Fetal Heart	heart
26	chr17:18094400-18114600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr17:18094600-18114600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr17:18094800-18097800	Weak transcription	NHLF	lung
29	chr17:18094800-18098200	Weak transcription	Fetal Lung	lung
30	chr17:18094800-18098200	Weak transcription	HSMM	muscle
31	chr17:18094800-18098600	Weak transcription	HSMMtube	muscle
32	chr17:18094800-18098600	Weak transcription	NH-A	brain
33	chr17:18094800-18101800	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr17:18094800-18103400	Strong transcription	Fetal Intestine Large	intestine
35	chr17:18095000-18097000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr17:18095000-18097000	Weak transcription	Gastric	stomach
37	chr17:18095000-18097000	Weak transcription	A549	lung
38	chr17:18095000-18097000	Weak transcription	K562	blood
39	chr17:18095000-18097400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
40	chr17:18095000-18097800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr17:18095000-18097800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr17:18095000-18097800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr17:18095000-18097800	Weak transcription	Fetal Brain Female	brain
44	chr17:18095000-18098200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr17:18095000-18098200	Weak transcription	Ovary	ovary
46	chr17:18095000-18108600	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr17:18095000-18114600	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr17:18095000-18114800	Strong transcription	Fetal Thymus	thymus
49	chr17:18095200-18097000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr17:18095200-18097000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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