Variant report

Variant	rs17751454
Chromosome Location	chr14:64625181-64625182
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17179404	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs17766755	0.80[CHB][hapmap]
rs2297301	0.90[CHB][hapmap];0.88[ASN][1000 genomes]
rs2772163	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs2781381	0.91[ASN][1000 genomes]
rs3866742	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4986938	0.80[CHB][hapmap]
rs61987290	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7148122	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs72720364	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8006145	0.80[CHB][hapmap]
rs867443	0.80[CHB][hapmap]
rs9919904	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv456326	chr14:64420413-64754361	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv564905	chr14:64420413-64754361	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17751454	MTHFD1	cis	parietal	SCAN
rs17751454	KCNH5	cis	parietal	SCAN
rs17751454	SLC38A6	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64567400-64647200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr14:64578200-64649000	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr14:64578600-64649000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr14:64581800-64650400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr14:64583400-64649000	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr14:64583600-64638000	Strong transcription	Placenta	Placenta
7	chr14:64586000-64649000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr14:64586400-64631800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr14:64590200-64634000	Weak transcription	HepG2	liver
10	chr14:64591000-64649000	Strong transcription	Liver	Liver
11	chr14:64594600-64653200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr14:64596400-64653000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr14:64597000-64626400	Weak transcription	Psoas Muscle	Psoas
14	chr14:64600600-64667400	Weak transcription	Stomach Mucosa	stomach
15	chr14:64606200-64627200	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr14:64606200-64647200	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr14:64609800-64633200	Weak transcription	Small Intestine	intestine
18	chr14:64609800-64636600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr14:64609800-64653000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr14:64610600-64625400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr14:64610600-64651000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr14:64612600-64640000	Strong transcription	Dnd41	blood
23	chr14:64612800-64640000	Strong transcription	Primary T cells from cord blood	blood
24	chr14:64613800-64635400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr14:64614000-64626800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr14:64614000-64628800	Weak transcription	Right Ventricle	heart
27	chr14:64614000-64635600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr14:64614200-64625200	Weak transcription	Lung	lung
29	chr14:64614200-64628800	Weak transcription	Gastric	stomach
30	chr14:64614200-64635400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr14:64614200-64636000	Weak transcription	Hela-S3	cervix
32	chr14:64614200-64637000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr14:64614400-64625400	Weak transcription	NHEK	skin
34	chr14:64614600-64626000	Weak transcription	Primary B cells from cord blood	blood
35	chr14:64614600-64631800	Weak transcription	NH-A	brain
36	chr14:64614800-64626200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr14:64614800-64644400	Weak transcription	HSMM	muscle
38	chr14:64616000-64628600	Weak transcription	Colonic Mucosa	Colon
39	chr14:64617400-64627000	Strong transcription	Duodenum Mucosa	Duodenum
40	chr14:64617600-64649000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr14:64617800-64627200	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr14:64617800-64649000	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr14:64620000-64626400	Weak transcription	Fetal Brain Male	brain
44	chr14:64620000-64629000	Weak transcription	Fetal Thymus	thymus
45	chr14:64620000-64634000	Weak transcription	Colon Smooth Muscle	Colon
46	chr14:64620000-64651200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr14:64620400-64625800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr14:64620400-64626200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr14:64620400-64626400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr14:64620400-64627600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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