Variant report

Variant	rs12051649
Chromosome Location	chr17:18117529-18117530
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs2075657	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2075658	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs2245430	0.91[CHB][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2473656	0.91[CHB][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2605133	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2856289	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4925144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59588957	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712271	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs712274	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72831919	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs854773	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs854774	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs854777	0.89[CEU][hapmap];0.86[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs854778	0.82[EUR][1000 genomes]
rs854780	0.82[EUR][1000 genomes]
rs854783	0.82[EUR][1000 genomes]
rs854796	0.93[ASN][1000 genomes]
rs854800	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs854802	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs854803	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9899249	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9903403	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9903591	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9913262	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1062828	chr17:18098110-18136330	Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv543245	chr17:18098110-18136330	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12051649	SHMT1	cis	Whole Blood	GTEx
rs12051649	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs12051649	SHMT1	cis	Muscle Skeletal	GTEx
rs12051649	SHMT1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18109400-18122200	Weak transcription	K562	blood
2	chr17:18109600-18117600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr17:18110600-18122200	Weak transcription	NHDF-Ad	bronchial
4	chr17:18112600-18127400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr17:18113000-18128200	Weak transcription	Small Intestine	intestine
6	chr17:18113200-18128200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr17:18113600-18121200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr17:18113600-18128000	Weak transcription	Colon Smooth Muscle	Colon
9	chr17:18113800-18122000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr17:18113800-18124400	Weak transcription	Hela-S3	cervix
11	chr17:18113800-18124600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:18113800-18127400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr17:18113800-18127400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr17:18113800-18128200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr17:18114000-18120800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:18114000-18121000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr17:18114200-18117600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr17:18114200-18118200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr17:18114200-18122000	Weak transcription	NH-A	brain
20	chr17:18114200-18122200	Weak transcription	Fetal Lung	lung
21	chr17:18114200-18122200	Weak transcription	HUVEC	blood vessel
22	chr17:18114200-18127400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr17:18114200-18127400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr17:18114200-18127400	Weak transcription	Left Ventricle	heart
25	chr17:18114400-18117600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr17:18114400-18117600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr17:18114400-18117600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr17:18114400-18117600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr17:18114400-18117600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr17:18114400-18117800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr17:18114400-18118200	Weak transcription	Primary T cells from cord blood	blood
32	chr17:18114400-18118200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr17:18114400-18120800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr17:18114400-18120800	Weak transcription	Brain Substantia Nigra	brain
35	chr17:18114400-18122200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr17:18114400-18127400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr17:18114400-18128200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr17:18114600-18118000	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr17:18114600-18118000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr17:18114600-18118000	Weak transcription	NHEK	skin
41	chr17:18114600-18118200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr17:18114600-18118200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr17:18114600-18118600	Weak transcription	Dnd41	blood
44	chr17:18114600-18118800	Weak transcription	Primary B cells from cord blood	blood
45	chr17:18114600-18119000	Weak transcription	Colonic Mucosa	Colon
46	chr17:18114600-18119000	Weak transcription	Fetal Intestine Large	intestine
47	chr17:18114600-18119600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr17:18114600-18120000	Weak transcription	Fetal Muscle Leg	muscle
49	chr17:18114600-18120600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr17:18114600-18120800	Weak transcription	Primary B cells from peripheral blood	blood

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