Variant report

Variant	rs55982711
Chromosome Location	chr17:46065402-46065403
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46065135..46066794-chr17:46070523..46072914,2	MCF-7	breast:
2	chr17:46064933..46067351-chr17:46077390..46079029,2	K562	blood:
3	chr17:46063889..46066659-chr17:46081400..46084023,2	MCF-7	breast:
4	chr17:46058631..46063478-chr17:46064617..46070061,8	K562	blood:
5	chr17:46050120..46053097-chr17:46063923..46066102,2	K562	blood:
6	chr17:46059948..46063060-chr17:46063175..46066138,4	MCF-7	breast:
7	chr17:46064874..46067902-chr17:46077258..46079817,3	K562	blood:
8	chr17:45912193..45915082-chr17:46064625..46066503,2	MCF-7	breast:
9	chr17:46047143..46050163-chr17:46062880..46067847,6	MCF-7	breast:
10	chr17:46059865..46061717-chr17:46063064..46066103,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12601350	0.85[EUR][1000 genomes]
rs12602131	0.85[EUR][1000 genomes]
rs12602670	0.85[EUR][1000 genomes]
rs1473117	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17616799	0.91[EUR][1000 genomes]
rs1986694	0.82[EUR][1000 genomes]
rs2023885	0.81[EUR][1000 genomes]
rs2229369	0.81[EUR][1000 genomes]
rs2240119	0.85[EUR][1000 genomes]
rs2240120	0.81[EUR][1000 genomes]
rs2285860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2325783	0.81[EUR][1000 genomes]
rs2525105	0.88[EUR][1000 genomes]
rs56402159	0.91[EUR][1000 genomes]
rs57782323	0.94[EUR][1000 genomes]
rs58554000	0.83[EUR][1000 genomes]
rs61396871	0.91[EUR][1000 genomes]
rs72823519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72823528	0.85[EUR][1000 genomes]
rs72823532	0.85[EUR][1000 genomes]
rs72823533	0.85[EUR][1000 genomes]
rs757353	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55982711	CDK5RAP3	cis	Nerve Tibial	GTEx
rs55982711	CBX1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46049800-46066600	Weak transcription	Small Intestine	intestine
2	chr17:46061600-46069200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr17:46061800-46065800	Weak transcription	K562	blood
4	chr17:46061800-46066000	Weak transcription	GM12878-XiMat	blood
5	chr17:46061800-46066600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr17:46061800-46068200	Weak transcription	NHLF	lung
7	chr17:46061800-46079600	Weak transcription	Right Atrium	heart
8	chr17:46062400-46067200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr17:46062800-46066200	Weak transcription	Fetal Thymus	thymus
10	chr17:46063000-46066600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr17:46063000-46066800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr17:46063000-46068200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr17:46063400-46068600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr17:46063400-46074200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr17:46063600-46065800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr17:46063600-46074600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr17:46063800-46065600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr17:46063800-46065600	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr17:46063800-46065600	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr17:46063800-46065600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr17:46063800-46065800	Enhancers	H1 Cell Line	embryonic stem cell
22	chr17:46063800-46068800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:46064000-46065600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr17:46064000-46065600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr17:46064000-46065600	Enhancers	Fetal Brain Male	brain
26	chr17:46064000-46065800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr17:46064000-46066400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr17:46064200-46066400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr17:46064200-46071000	Enhancers	HSMMtube	muscle
30	chr17:46064400-46065600	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr17:46064400-46065600	Enhancers	Fetal Brain Female	brain
32	chr17:46064400-46065600	Enhancers	Placenta	Placenta
33	chr17:46064400-46065600	Enhancers	HepG2	liver
34	chr17:46064400-46066200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
35	chr17:46064400-46066400	Enhancers	Fetal Intestine Small	intestine
36	chr17:46064400-46067000	Enhancers	Fetal Muscle Leg	muscle
37	chr17:46064600-46065600	Bivalent Enhancer	Fetal Stomach	stomach
38	chr17:46064600-46065600	Enhancers	HSMM	muscle
39	chr17:46064600-46065600	Enhancers	NHDF-Ad	bronchial
40	chr17:46064600-46065800	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr17:46064600-46065800	Enhancers	Brain Germinal Matrix	brain
42	chr17:46064600-46066200	Enhancers	Fetal Intestine Large	intestine
43	chr17:46064600-46066600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr17:46064800-46071400	Weak transcription	Pancreas	Pancrea
45	chr17:46065000-46065800	Enhancers	Spleen	Spleen
46	chr17:46065200-46065600	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr17:46065200-46066400	Enhancers	Fetal Muscle Trunk	muscle
48	chr17:46065200-46068000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr17:46065200-46068200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr17:46065200-46068200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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