Variant report

Variant	rs2772163
Chromosome Location	chr14:64693385-64693386
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64690892..64693639-chr14:64700268..64702860,3	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs17179404	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17751454	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs17766755	1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap]
rs3020443	0.80[CHB][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs35648226	0.83[AMR][1000 genomes]
rs4986938	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs7148637	0.80[MEX][hapmap]
rs7154455	0.80[MEX][hapmap]
rs72720395	0.88[ASN][1000 genomes]
rs8006145	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs867443	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs9919904	0.80[CHB][hapmap];0.82[JPT][hapmap]

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	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
4	nsv902021	chr14:64647646-64715794	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv1050378	chr14:64686543-64703012	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2772163	MTHFD1	cis	parietal	SCAN
rs2772163	SLC38A6	cis	cerebellum	SCAN
rs2772163	KCNH5	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64664000-64699600	Weak transcription	Small Intestine	intestine
2	chr14:64664200-64698600	Weak transcription	HMEC	breast
3	chr14:64665400-64700200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr14:64666800-64699400	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr14:64672800-64696600	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr14:64674600-64696000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr14:64674600-64696200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr14:64674600-64696400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr14:64674600-64699800	Strong transcription	Liver	Liver
10	chr14:64674800-64695800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr14:64674800-64696000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr14:64674800-64696000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr14:64674800-64696000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr14:64674800-64696200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr14:64674800-64696200	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr14:64674800-64696200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr14:64674800-64696400	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr14:64674800-64696400	Strong transcription	Dnd41	blood
19	chr14:64674800-64696800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr14:64674800-64697600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr14:64674800-64698400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr14:64674800-64699000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr14:64674800-64700000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr14:64674800-64700600	Strong transcription	Fetal Intestine Large	intestine
25	chr14:64675000-64696400	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr14:64675000-64696400	Strong transcription	Brain Germinal Matrix	brain
27	chr14:64675200-64696400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr14:64675400-64695200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr14:64675400-64696200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr14:64676600-64696200	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr14:64676800-64698800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr14:64677000-64698600	Weak transcription	NHLF	lung
33	chr14:64677000-64698800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr14:64677000-64699400	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr14:64677200-64698600	Weak transcription	NHDF-Ad	bronchial
36	chr14:64677400-64697800	Strong transcription	Fetal Stomach	stomach
37	chr14:64677600-64698200	Strong transcription	Colonic Mucosa	Colon
38	chr14:64679800-64698200	Weak transcription	HUVEC	blood vessel
39	chr14:64679800-64698800	Weak transcription	NH-A	brain
40	chr14:64680600-64694800	Strong transcription	Fetal Intestine Small	intestine
41	chr14:64681600-64698800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr14:64684400-64696800	Strong transcription	Adipose Nuclei	Adipose
43	chr14:64684400-64699600	Strong transcription	Placenta	Placenta
44	chr14:64684600-64696600	Strong transcription	Fetal Brain Female	brain
45	chr14:64684600-64696800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr14:64685200-64696000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr14:64685400-64696000	Strong transcription	Fetal Lung	lung
48	chr14:64685800-64696200	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr14:64686000-64694400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr14:64686000-64696200	Strong transcription	Lung	lung

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