Variant report

Variant	rs61454280
Chromosome Location	chr17:46050125-46050126
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr17:46047522-46050410	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr17:46049424-46050825	K562	blood:	n/a	n/a
3	MXI1	chr17:46047255-46050557	SK-N-SH	brain:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45916805..45918645-chr17:46049307..46052220,2	MCF-7	breast:
2	chr17:46047400..46050259-chr17:46124707..46126731,3	MCF-7	breast:
3	chr17:46048621..46050545-chr17:46057076..46059668,3	K562	blood:
4	chr17:46033549..46039001-chr17:46046732..46050276,6	K562	blood:
5	chr17:46017765..46021634-chr17:46045854..46051133,6	MCF-7	breast:
6	chr17:45971266..45974117-chr17:46049059..46051074,2	MCF-7	breast:
7	chr17:45971215..45974947-chr17:46046480..46050487,6	MCF-7	breast:
8	chr17:46031321..46037809-chr17:46043555..46050276,13	K562	blood:
9	chr17:46023026..46029175-chr17:46044937..46051234,10	K562	blood:
10	chr17:46048432..46050374-chr17:46050535..46053358,3	MCF-7	breast:
11	chr17:46048551..46050173-chr17:46123931..46126830,2	MCF-7	breast:
12	chr17:46047245..46051740-chr17:46053378..46057507,6	MCF-7	breast:
13	chr17:46048621..46053225-chr17:46056317..46060413,5	K562	blood:
14	chr17:45971907..45976557-chr17:46046916..46050358,7	K562	blood:
15	chr17:46047439..46051573-chr17:46055956..46059590,5	MCF-7	breast:
16	chr17:46048370..46050701-chr17:46124898..46126529,2	K562	blood:

No data

Variant related genes	Relation type
CDK5RAP3	TF binding region
ENSG00000082641	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000264019	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000263412	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs72823509	1.00[ASN][1000 genomes]
rs72823513	1.00[ASN][1000 genomes]
rs8067216	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs61454280	CDK5RAP3	cis	Artery Tibial	GTEx
rs61454280	CDK5RAP3	cis	Nerve Tibial	GTEx
rs61454280	SKAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46049000-46050400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr17:46049000-46050400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr17:46049000-46050400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
4	chr17:46049000-46050800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr17:46049000-46050800	Weak transcription	Gastric	stomach
6	chr17:46049000-46051000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr17:46049000-46051200	Weak transcription	Aorta	Aorta
8	chr17:46049000-46051600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr17:46049000-46052200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:46049000-46055200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr17:46049000-46056000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr17:46049200-46050400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr17:46049200-46050400	Enhancers	Primary B cells from peripheral blood	blood
14	chr17:46049200-46050400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr17:46049200-46050400	Enhancers	Fetal Muscle Leg	muscle
16	chr17:46049200-46051000	Weak transcription	Left Ventricle	heart
17	chr17:46049200-46051200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr17:46049200-46051200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr17:46049200-46051400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr17:46049200-46051600	Weak transcription	Fetal Kidney	kidney
21	chr17:46049400-46050200	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr17:46049400-46050200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr17:46049400-46050200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr17:46049400-46050200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr17:46049400-46050400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr17:46049400-46050400	Enhancers	Primary T cells fromperipheralblood	blood
27	chr17:46049400-46050400	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr17:46049400-46050400	Enhancers	Brain Substantia Nigra	brain
29	chr17:46049400-46050400	Enhancers	Pancreas	Pancrea
30	chr17:46049400-46050400	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr17:46049400-46050400	Flanking Active TSS	GM12878-XiMat	blood
32	chr17:46049400-46050800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr17:46049400-46050800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr17:46049400-46050800	Weak transcription	Lung	lung
35	chr17:46049400-46051000	Weak transcription	Esophagus	oesophagus
36	chr17:46049400-46051000	Weak transcription	Placenta	Placenta
37	chr17:46049400-46051000	Enhancers	Fetal Thymus	thymus
38	chr17:46049400-46051200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr17:46049400-46052800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr17:46049600-46050200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr17:46049600-46050200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr17:46049600-46050200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr17:46049600-46050200	Weak transcription	Fetal Stomach	stomach
44	chr17:46049600-46050200	Enhancers	Ovary	ovary
45	chr17:46049600-46050200	Transcr. at gene 5' and 3'	K562	blood
46	chr17:46049600-46050400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr17:46049600-46050400	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr17:46049600-46050400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr17:46049600-46050400	Enhancers	Brain Hippocampus Middle	brain
50	chr17:46049600-46050400	Enhancers	Duodenum Mucosa	Duodenum

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