Variant report

Variant	rs17249444
Chromosome Location	chr14:68101454-68101455
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:68100621..68105331-chr14:68105570..68110001,8	K562	blood:
2	chr14:68086561..68088092-chr14:68100467..68103078,2	K562	blood:
3	chr14:68085085..68089308-chr14:68100128..68104989,9	K562	blood:

Variant related genes	Relation type
ENSG00000081181	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10136206	0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10483802	0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12100925	0.81[ASN][1000 genomes]
rs12432546	0.81[ASN][1000 genomes]
rs12434923	0.82[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12435352	0.82[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12435531	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs12435927	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12436474	0.98[ASN][1000 genomes]
rs12437263	0.81[ASN][1000 genomes]
rs12587111	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12590038	0.81[ASN][1000 genomes]
rs12590620	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs15493	0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs17249563	0.81[ASN][1000 genomes]
rs1804799	0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2009590	0.82[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs3759768	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs56246064	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56981676	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58588003	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58668895	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6573788	0.89[MEX][hapmap];0.81[MKK][hapmap]
rs8010798	0.82[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs8012815	0.88[MEX][hapmap];0.82[MKK][hapmap]
rs910315	0.82[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456331	chr14:67732861-68103780	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv564961	chr14:67732861-68103780	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers 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	41 gene(s)	inside rSNPs	diseases
3	nsv470651	chr14:67732861-68113293	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv902066	chr14:67873128-68103780	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv902068	chr14:68083133-68204876	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17249444	MTHFD1	cis	parietal	SCAN
rs17249444	FUT8	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68087200-68109600	Weak transcription	Gastric	stomach
2	chr14:68087200-68112400	Weak transcription	Aorta	Aorta
3	chr14:68087800-68112000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr14:68088000-68112400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr14:68088000-68112400	Weak transcription	Brain Angular Gyrus	brain
6	chr14:68088000-68112600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:68088800-68123000	Weak transcription	Fetal Brain Male	brain
8	chr14:68089400-68112200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr14:68089600-68116200	Weak transcription	Fetal Kidney	kidney
10	chr14:68089800-68103000	Weak transcription	Brain Hippocampus Middle	brain
11	chr14:68089800-68113400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr14:68090000-68109800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr14:68090000-68114800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr14:68090000-68115800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr14:68090200-68102600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr14:68090200-68102800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr14:68090200-68110400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr14:68090200-68111000	Weak transcription	Colon Smooth Muscle	Colon
19	chr14:68090200-68112000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr14:68090200-68112200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr14:68090200-68112400	Weak transcription	Brain Anterior Caudate	brain
22	chr14:68090400-68102800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr14:68090400-68112200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr14:68090800-68102200	Weak transcription	Psoas Muscle	Psoas
25	chr14:68090800-68103000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr14:68090800-68110000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr14:68090800-68111200	Weak transcription	HUVEC	blood vessel
28	chr14:68090800-68111800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr14:68090800-68112200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr14:68091000-68103000	Weak transcription	Hela-S3	cervix
31	chr14:68091800-68109000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr14:68091800-68111000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr14:68091800-68112200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr14:68091800-68116600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr14:68092000-68102000	Weak transcription	NHEK	skin
36	chr14:68092000-68112400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr14:68096600-68112400	Weak transcription	HepG2	liver
38	chr14:68098000-68102800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr14:68098000-68110000	Weak transcription	Brain Germinal Matrix	brain
40	chr14:68099200-68102800	Weak transcription	Fetal Intestine Small	intestine
41	chr14:68100000-68112200	Weak transcription	Pancreas	Pancrea
42	chr14:68100600-68101600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr14:68100600-68103000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr14:68100600-68114600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr14:68100800-68101600	Weak transcription	K562	blood
46	chr14:68100800-68109000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr14:68100800-68112200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr14:68100800-68112200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr14:68101000-68109800	Weak transcription	Fetal Brain Female	brain
50	chr14:68101400-68102000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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