Variant report

Variant	rs2256020
Chromosome Location	chr17:46050635-46050636
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:46050502-46050978	HepG2	liver:	n/a	n/a
2	POLR2A	chr17:46049424-46050825	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45916805..45918645-chr17:46049307..46052220,2	MCF-7	breast:
2	chr17:46048432..46050374-chr17:46050535..46053358,3	MCF-7	breast:
3	chr17:46017765..46021634-chr17:46045854..46051133,6	MCF-7	breast:
4	chr17:45971266..45974117-chr17:46049059..46051074,2	MCF-7	breast:
5	chr17:46023026..46029175-chr17:46044937..46051234,10	K562	blood:
6	chr17:46047245..46051740-chr17:46053378..46057507,6	MCF-7	breast:
7	chr17:46048621..46053225-chr17:46056317..46060413,5	K562	blood:
8	chr17:46047439..46051573-chr17:46055956..46059590,5	MCF-7	breast:
9	chr17:46048370..46050701-chr17:46124898..46126529,2	K562	blood:

No data

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

Extended variants
information (count: 19 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11079800	0.82[ASW][hapmap];1.00[YRI][hapmap]
rs1317850	0.82[CEU][hapmap]
rs16949418	0.82[YRI][hapmap]
rs2255814	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2325748	0.82[YRI][hapmap]
rs2525083	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2525097	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2597164	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2597177	0.83[CHB][hapmap]
rs2597178	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2737	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4794331	0.91[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7216411	0.84[ASW][hapmap];0.82[CEU][hapmap];0.91[CHB][hapmap];0.83[MEX][hapmap]
rs736387	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs757352	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs8076163	0.82[CEU][hapmap]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2256020	ATP6V0A1	cis	parietal	SCAN
rs2256020	NFE2L1	cis	cerebellum	SCAN
rs2256020	DUSP3	cis	parietal	SCAN
rs2256020	VAT1	cis	cerebellum	SCAN
rs2256020	CDK5RAP3	cis	Whole Blood	GTEx
rs2256020	RP11-6N17.10	cis	Whole Blood	GTEx
rs2256020	SP2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46049000-46050800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr17:46049000-46050800	Weak transcription	Gastric	stomach
3	chr17:46049000-46051000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:46049000-46051200	Weak transcription	Aorta	Aorta
5	chr17:46049000-46051600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr17:46049000-46052200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:46049000-46055200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr17:46049000-46056000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr17:46049200-46051000	Weak transcription	Left Ventricle	heart
10	chr17:46049200-46051200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr17:46049200-46051200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr17:46049200-46051400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr17:46049200-46051600	Weak transcription	Fetal Kidney	kidney
14	chr17:46049400-46050800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr17:46049400-46050800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr17:46049400-46050800	Weak transcription	Lung	lung
17	chr17:46049400-46051000	Weak transcription	Esophagus	oesophagus
18	chr17:46049400-46051000	Weak transcription	Placenta	Placenta
19	chr17:46049400-46051000	Enhancers	Fetal Thymus	thymus
20	chr17:46049400-46051200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr17:46049400-46052800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr17:46049600-46050800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr17:46049600-46050800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr17:46049600-46050800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr17:46049600-46050800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr17:46049600-46051000	Weak transcription	Primary B cells from cord blood	blood
27	chr17:46049600-46051000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr17:46049600-46051000	Weak transcription	Brain Germinal Matrix	brain
29	chr17:46049600-46051200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr17:46049600-46051200	Weak transcription	HSMMtube	muscle
31	chr17:46049600-46051400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr17:46049600-46051400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr17:46049600-46052800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr17:46049600-46056200	Weak transcription	Psoas Muscle	Psoas
35	chr17:46049600-46059600	Weak transcription	Fetal Heart	heart
36	chr17:46049800-46050800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr17:46049800-46050800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr17:46049800-46050800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr17:46049800-46050800	Weak transcription	Brain Anterior Caudate	brain
40	chr17:46049800-46050800	Weak transcription	HMEC	breast
41	chr17:46049800-46051000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr17:46049800-46051000	Weak transcription	Primary T cells from cord blood	blood
43	chr17:46049800-46051000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr17:46049800-46051000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr17:46049800-46051000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr17:46049800-46051000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr17:46049800-46051200	Weak transcription	HUVEC	blood vessel
48	chr17:46049800-46051400	Weak transcription	Fetal Lung	lung
49	chr17:46049800-46051600	Weak transcription	Colon Smooth Muscle	Colon
50	chr17:46049800-46052200	Weak transcription	NH-A	brain

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