Variant report

Variant	rs9508646
Chromosome Location	chr13:30706303-30706304
allele	A/C
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	chr13:30698648..30700274-chr13:30705836..30708500,2	MCF-7	breast:
3	chr13:30705361..30707918-chr13:31032869..31034442,2	K562	blood:

Variant related genes	Relation type
ENSG00000102781	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs4769028	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4769808	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4769810	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs533910	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs533937	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs549744	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs584999	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs585049	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs641545	0.85[CEU][hapmap];0.85[CHB][hapmap];0.82[TSI][hapmap]
rs66587785	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7334284	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7334437	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7984451	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8000970	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9506264	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9506265	0.84[EUR][1000 genomes]
rs9506266	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9508639	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9508641	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9508642	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9508643	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9508644	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9508647	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:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9508646	EEF1DP3	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30694400-30707000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:30696400-30707000	Weak transcription	Thymus	Thymus
3	chr13:30700200-30707000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr13:30700200-30708000	Weak transcription	NH-A	brain
5	chr13:30700200-30717200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr13:30700800-30706800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr13:30701400-30707000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr13:30701400-30707000	Weak transcription	NHDF-Ad	bronchial
9	chr13:30701600-30706400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr13:30701600-30706600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr13:30701600-30707000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr13:30701800-30706800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr13:30701800-30707000	Weak transcription	Osteobl	bone
14	chr13:30702000-30706800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr13:30702200-30706600	Weak transcription	Colon Smooth Muscle	Colon
16	chr13:30702200-30707000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr13:30702200-30707000	Weak transcription	Gastric	stomach
18	chr13:30702200-30707000	Weak transcription	Left Ventricle	heart
19	chr13:30702400-30706600	Weak transcription	Stomach Mucosa	stomach
20	chr13:30702600-30706600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr13:30703200-30706600	Weak transcription	Fetal Thymus	thymus
22	chr13:30703200-30707000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr13:30703200-30707000	Weak transcription	GM12878-XiMat	blood
24	chr13:30704000-30706400	Weak transcription	Dnd41	blood
25	chr13:30704000-30707000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr13:30705600-30706800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr13:30705800-30706600	Weak transcription	Brain Cingulate Gyrus	brain

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