Variant report

Variant	rs746899
Chromosome Location	chr17:17426009-17426010
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr17:17426006-17427055	HEK293-T-REx	kidney:	n/a	chr17:17426221-17426242 chr17:17426232-17426241

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17417655..17420606-chr17:17424227..17426115,2	K562	blood:
2	chr17:17422447..17424302-chr17:17424957..17427591,2	MCF-7	breast:

Variant related genes	Relation type
PEMT	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11078389	0.81[CEU][hapmap]
rs1109859	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs11651620	0.92[CEU][hapmap]
rs12935886	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12948060	0.81[CEU][hapmap]
rs2124344	0.81[CEU][hapmap]
rs2168345	0.98[EUR][1000 genomes]
rs4244592	0.98[EUR][1000 genomes]
rs4244593	1.00[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs4244594	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4244596	0.81[CEU][hapmap]
rs4244598	0.81[CEU][hapmap]
rs4646350	0.81[CEU][hapmap]
rs4646385	0.84[CEU][hapmap]
rs4646387	0.92[CEU][hapmap]
rs4646389	0.92[CEU][hapmap]
rs4646390	0.95[CEU][hapmap]
rs4646391	0.92[CEU][hapmap]
rs4646392	0.92[CEU][hapmap]
rs4646397	0.87[CEU][hapmap]
rs4646402	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4646405	0.88[CEU][hapmap];0.95[EUR][1000 genomes]
rs4924922	0.96[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs6502603	0.92[CEU][hapmap]
rs729975	0.81[CEU][hapmap]
rs747770	0.96[CEU][hapmap]
rs748196	0.96[CEU][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs750546	0.85[CEU][hapmap]
rs8082417	0.84[CEU][hapmap]
rs897451	0.80[CEU][hapmap]
rs936108	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482648	chr17:17315268-17455442	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv907731	chr17:17358004-17504856	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv907735	chr17:17381764-17448589	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv907736	chr17:17381764-17465458	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv907741	chr17:17404586-17429927	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv907742	chr17:17404586-17432744	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv907743	chr17:17404586-17448589	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv907744	chr17:17404586-17504856	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	esv1803680	chr17:17408484-17426009	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv907745	chr17:17411211-17429927	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv907746	chr17:17412032-17478917	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv907747	chr17:17412032-17504856	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
14	nsv523094	chr17:17415217-17430649	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv907749	chr17:17417169-17448589	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv524158	chr17:17420199-17430649	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv574526	chr17:17422608-17444369	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	nsv470579	chr17:17424332-17493810	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs746899	SLC47A1	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17410200-17426400	Weak transcription	Fetal Intestine Large	intestine
2	chr17:17411000-17428600	Weak transcription	Brain Hippocampus Middle	brain
3	chr17:17411000-17428600	Weak transcription	Right Atrium	heart
4	chr17:17411000-17428800	Weak transcription	Brain Anterior Caudate	brain
5	chr17:17411400-17428600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr17:17413200-17437400	Weak transcription	Aorta	Aorta
7	chr17:17417600-17429400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr17:17418200-17478000	Weak transcription	Primary T cells from cord blood	blood
9	chr17:17419200-17426200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:17419400-17426400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr17:17419400-17430800	Weak transcription	Placenta	Placenta
12	chr17:17419600-17447000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr17:17419800-17426800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr17:17420000-17426400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr17:17420000-17426400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr17:17420000-17426400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr17:17420000-17426600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr17:17420000-17427000	Weak transcription	HepG2	liver
19	chr17:17420000-17428600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr17:17420000-17429600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr17:17420000-17429800	Weak transcription	Right Ventricle	heart
22	chr17:17420400-17426200	Strong transcription	Fetal Intestine Small	intestine
23	chr17:17420600-17426400	Weak transcription	Stomach Mucosa	stomach
24	chr17:17420600-17434400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr17:17421000-17439200	Weak transcription	HSMM	muscle
26	chr17:17421800-17427600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr17:17424000-17426800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr17:17424400-17426600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr17:17424600-17426800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr17:17424600-17426800	Weak transcription	Fetal Brain Female	brain
31	chr17:17424600-17460000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr17:17424800-17426200	Weak transcription	Ovary	ovary
33	chr17:17424800-17426600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr17:17424800-17428600	Weak transcription	Esophagus	oesophagus
35	chr17:17424800-17428800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr17:17424800-17429600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr17:17425000-17426200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr17:17425000-17430800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr17:17425000-17431200	Weak transcription	Spleen	Spleen
40	chr17:17425200-17427000	Enhancers	Fetal Thymus	thymus
41	chr17:17425200-17427800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr17:17425400-17426400	Weak transcription	Lung	lung
43	chr17:17425400-17427000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr17:17425400-17427200	Enhancers	Fetal Muscle Trunk	muscle
45	chr17:17425400-17427600	Enhancers	Pancreas	Pancrea
46	chr17:17425400-17429800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr17:17425600-17426200	Weak transcription	Thymus	Thymus
48	chr17:17425600-17426400	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr17:17425600-17426600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr17:17425600-17427000	Enhancers	H1 Cell Line	embryonic stem cell

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