Variant report

Variant	rs9508647
Chromosome Location	chr13:30708574-30708575
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	13:30704196-30711562..13:30879528-30882380	H1-hESC	embryonic stem cell:	embryo
2	chr13:30707361..30710289-chr13:30714464..30717739,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102781	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs4769028	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4769808	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4769810	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs531266	0.81[EUR][1000 genomes]
rs533910	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533937	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs549744	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs584999	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585049	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641545	0.85[CEU][hapmap];0.85[CHB][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs66587785	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7334284	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334437	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7984451	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8000970	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9506264	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9506265	0.83[EUR][1000 genomes]
rs9506266	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9508639	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9508641	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9508642	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9508643	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9508644	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9508646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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	nsv1040215	chr13:30621351-30741022	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv541745	chr13:30621351-30741022	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv832572	chr13:30650005-30835256	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv981	chr13:30703159-30739838	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv1847946	chr13:30707385-30731192	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9508647	EEF1DP3	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30700200-30717200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr13:30706400-30709400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr13:30706600-30708800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr13:30706600-30708800	Enhancers	Stomach Mucosa	stomach
5	chr13:30706600-30709000	Enhancers	Brain Hippocampus Middle	brain
6	chr13:30706600-30709000	Enhancers	Brain Substantia Nigra	brain
7	chr13:30706600-30709200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr13:30706600-30709200	Enhancers	Fetal Intestine Small	intestine
9	chr13:30706800-30708600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr13:30706800-30708600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr13:30706800-30708600	Enhancers	Fetal Muscle Leg	muscle
12	chr13:30706800-30709600	Enhancers	Adipose Nuclei	Adipose
13	chr13:30707000-30708800	Enhancers	HSMM	muscle
14	chr13:30707000-30708800	Enhancers	NHDF-Ad	bronchial
15	chr13:30707000-30709000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr13:30707000-30709000	Enhancers	Fetal Intestine Large	intestine
17	chr13:30707000-30709200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr13:30707000-30709400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr13:30707000-30709400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr13:30707000-30709400	Enhancers	Ovary	ovary
21	chr13:30707000-30709400	Enhancers	Osteobl	bone
22	chr13:30707000-30710000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr13:30707000-30710000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr13:30707200-30708600	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr13:30707200-30708600	Enhancers	HSMMtube	muscle
26	chr13:30707200-30708800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr13:30707200-30708800	Enhancers	Brain Cingulate Gyrus	brain
28	chr13:30707200-30708800	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr13:30707200-30709200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr13:30707200-30712200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr13:30707200-30712400	Weak transcription	Fetal Lung	lung
32	chr13:30707400-30709200	Enhancers	Stomach Smooth Muscle	stomach
33	chr13:30707400-30714400	Weak transcription	Spleen	Spleen
34	chr13:30707400-30714400	Weak transcription	GM12878-XiMat	blood
35	chr13:30707600-30708800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr13:30707600-30709000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr13:30707600-30712200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr13:30707800-30708600	Enhancers	NHLF	lung
39	chr13:30707800-30715200	Weak transcription	Dnd41	blood
40	chr13:30708000-30708600	Enhancers	NH-A	brain
41	chr13:30708000-30714400	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr13:30708200-30708600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr13:30708200-30708600	Weak transcription	Brain Anterior Caudate	brain
44	chr13:30708200-30708800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr13:30708200-30708800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr13:30708200-30709000	Enhancers	Rectal Smooth Muscle	rectum
47	chr13:30708400-30708600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr13:30708400-30708600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr13:30708400-30708600	Enhancers	Colon Smooth Muscle	Colon
50	chr13:30708400-30708600	Bivalent Enhancer	HepG2	liver

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