Variant report

Variant	rs753414
Chromosome Location	chr15:45474371-45474372
allele	A/C
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	MAX	chr15:45474190-45474453	NB4	blood:	n/a	n/a
2	EP300	chr15:45473575-45474754	SK-N-SH	brain:	n/a	chr15:45473859-45473873
3	MXI1	chr15:45473922-45475106	SK-N-SH	brain:	n/a	n/a
4	EP300	chr15:45474102-45474400	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:45472426..45475821-chr15:45489773..45493159,3	K562	blood:
2	chr15:45472426..45474381-chr15:45491659..45493233,2	K562	blood:
3	chr15:45471561..45475350-chr15:45693833..45697444,3	MCF-7	breast:
4	chr15:45472971..45475470-chr15:45491028..45492942,2	MCF-7	breast:

Variant related genes	Relation type
SHF	TF binding region
ENSG00000171763	Chromatin interaction
ENSG00000171766	Chromatin interaction
ENSG00000259932	Chromatin interaction
ENSG00000138606	Chromatin interaction
ENSG00000260035	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12323957	0.82[CHB][hapmap]
rs12438755	0.88[TSI][hapmap]
rs12592055	0.82[CHD][hapmap]
rs12899786	0.88[TSI][hapmap]
rs12904079	0.88[ASN][1000 genomes]
rs12909987	0.85[CHD][hapmap]
rs1648311	0.85[TSI][hapmap]
rs2292467	0.88[TSI][hapmap]
rs2458236	0.81[TSI][hapmap]
rs3959644	0.82[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.88[ASN][1000 genomes]
rs62026661	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62026665	0.85[ASN][1000 genomes]
rs62026666	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv427961	chr15:45338381-45491634	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	esv1823029	chr15:45387102-45482245	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription 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	76 gene(s)	inside rSNPs	diseases
6	nsv904187	chr15:45438537-45507738	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs753414	SHF	cis	parietal	SCAN
rs753414	SHF	cis	cerebellum	SCAN
rs753414	ADAL	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45459800-45478000	Weak transcription	Aorta	Aorta
2	chr15:45460000-45474800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:45460000-45477200	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr15:45460000-45478600	Weak transcription	Thymus	Thymus
5	chr15:45460200-45478000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr15:45460400-45475200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:45460600-45475400	Weak transcription	Brain Anterior Caudate	brain
8	chr15:45460600-45475600	Weak transcription	Left Ventricle	heart
9	chr15:45460600-45478000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:45460600-45478200	Weak transcription	Adipose Nuclei	Adipose
11	chr15:45462200-45477200	Weak transcription	Brain Hippocampus Middle	brain
12	chr15:45466000-45478800	Weak transcription	Right Ventricle	heart
13	chr15:45466400-45477600	Weak transcription	Colon Smooth Muscle	Colon
14	chr15:45467600-45476200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr15:45467600-45477400	Weak transcription	Brain Angular Gyrus	brain
16	chr15:45467800-45477400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr15:45468000-45477800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:45470200-45475600	Weak transcription	Placenta	Placenta
19	chr15:45470400-45475400	Weak transcription	Fetal Lung	lung
20	chr15:45470400-45476800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:45470600-45475200	Weak transcription	Liver	Liver
22	chr15:45470600-45475400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:45470600-45475800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:45471400-45474400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr15:45471400-45477000	Enhancers	HSMM	muscle
26	chr15:45471400-45477400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr15:45471600-45474600	Enhancers	Fetal Muscle Trunk	muscle
28	chr15:45471600-45478000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:45471800-45474600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:45471800-45475200	Enhancers	Fetal Muscle Leg	muscle
31	chr15:45471800-45478000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr15:45472000-45476000	Enhancers	HSMMtube	muscle
33	chr15:45472200-45475200	Weak transcription	Fetal Intestine Large	intestine
34	chr15:45472200-45476800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr15:45472400-45475200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:45472600-45475000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr15:45472800-45475200	Weak transcription	Ovary	ovary
38	chr15:45472800-45477400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:45473000-45476400	Enhancers	Primary hematopoietic stem cells	blood
40	chr15:45473000-45478200	Weak transcription	NH-A	brain
41	chr15:45473200-45474400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr15:45473200-45474400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr15:45473200-45474400	Strong transcription	Fetal Stomach	stomach
44	chr15:45473200-45477400	Enhancers	Fetal Brain Male	brain
45	chr15:45473200-45478200	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr15:45473200-45480400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr15:45473400-45474400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr15:45473400-45474400	Weak transcription	HepG2	liver
49	chr15:45473400-45476000	Weak transcription	Gastric	stomach
50	chr15:45473400-45476600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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