Variant report

Variant	rs57768342
Chromosome Location	chr17:46028625-46028626
allele	A/G
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:6)
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	POLR2A	chr17:46028579-46028717	MCF-7	breast:	n/a	n/a
2	POLR2A	chr17:46028561-46029330	HepG2	liver:	n/a	n/a
3	POLR2A	chr17:46028493-46028660	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46026192..46029068-chr17:46087372..46089166,2	K562	blood:
2	chr17:46028612..46030985-chr17:46062999..46064940,2	MCF-7	breast:
3	chr17:46027611..46030432-chr17:46048552..46050466,2	K562	blood:
4	chr17:46023026..46029175-chr17:46044937..46051234,10	K562	blood:
5	chr17:45968434..45977260-chr17:46017847..46029594,27	MCF-7	breast:
6	chr17:46027110..46029262-chr17:46094448..46097370,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000264019	TF binding region
ENSG00000108465	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000264920	Chromatin interaction

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

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

rs_ID	r²[population]
rs11079802	0.84[ASN][1000 genomes]
rs11651753	0.92[ASN][1000 genomes]
rs16949720	0.87[ASN][1000 genomes]
rs2002136	0.90[ASN][1000 genomes]
rs2255814	0.97[EUR][1000 genomes]
rs2428608	0.90[ASN][1000 genomes]
rs2525083	0.96[EUR][1000 genomes]
rs2525095	0.97[ASN][1000 genomes]
rs2525097	0.80[EUR][1000 genomes]
rs2525109	0.92[ASN][1000 genomes]
rs2525110	0.92[ASN][1000 genomes]
rs2597164	0.82[EUR][1000 genomes]
rs2597169	0.95[ASN][1000 genomes]
rs2597178	0.83[EUR][1000 genomes]
rs2737	0.85[EUR][1000 genomes]
rs2875735	0.95[ASN][1000 genomes]
rs3764398	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3826396	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4793738	0.94[ASN][1000 genomes]
rs4794331	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61665404	0.95[ASN][1000 genomes]
rs72823505	0.99[ASN][1000 genomes]
rs736387	0.85[EUR][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	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	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	esv1000014	chr17:46019228-46029457	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57768342	CDK5RAP3	cis	Whole Blood	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019800-46034200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
3	chr17:46020000-46034600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr17:46023200-46030000	Genic enhancers	Fetal Intestine Large	intestine
5	chr17:46024400-46031600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr17:46027000-46030000	Weak transcription	Psoas Muscle	Psoas
7	chr17:46027200-46029200	Genic enhancers	Fetal Intestine Small	intestine
8	chr17:46027200-46030000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr17:46027200-46031200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr17:46027200-46032600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr17:46027200-46034400	Weak transcription	Hela-S3	cervix
12	chr17:46027200-46047200	Weak transcription	Spleen	Spleen
13	chr17:46027400-46029600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr17:46027400-46029600	Weak transcription	Lung	lung
15	chr17:46027400-46030000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr17:46027400-46030000	Genic enhancers	Stomach Mucosa	stomach
17	chr17:46027400-46030800	Strong transcription	Fetal Stomach	stomach
18	chr17:46027400-46032600	Weak transcription	NHLF	lung
19	chr17:46027400-46033800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr17:46027400-46033800	Weak transcription	NHDF-Ad	bronchial
21	chr17:46027400-46034000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr17:46027400-46034200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr17:46027400-46034400	Weak transcription	Fetal Lung	lung
24	chr17:46027400-46034600	Weak transcription	K562	blood
25	chr17:46027400-46034800	Weak transcription	NH-A	brain
26	chr17:46027600-46028800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr17:46027600-46028800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr17:46027600-46028800	Weak transcription	Brain Anterior Caudate	brain
29	chr17:46027600-46029000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr17:46027600-46029000	Enhancers	Pancreas	Pancrea
31	chr17:46027600-46029000	Genic enhancers	Rectal Mucosa Donor 29	rectum
32	chr17:46027600-46029200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr17:46027600-46029800	Genic enhancers	Rectal Mucosa Donor 31	rectum
34	chr17:46027600-46030200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr17:46027600-46030400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr17:46027600-46030400	Enhancers	Liver	Liver
37	chr17:46027600-46030400	Weak transcription	Brain Substantia Nigra	brain
38	chr17:46027600-46031600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr17:46027600-46032200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr17:46027600-46032600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr17:46027600-46033000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr17:46027600-46033800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr17:46027600-46034200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr17:46027600-46034400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr17:46027600-46034800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr17:46027600-46047400	Weak transcription	Right Ventricle	heart
47	chr17:46027600-46047600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr17:46027800-46028800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr17:46027800-46029200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr17:46027800-46029600	Weak transcription	Primary T cells from cord blood	blood

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