Variant report

Variant	rs17703779
Chromosome Location	chr2:183895919-183895920
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:183848253..183851068-chr2:183895481..183897989,2	K562	blood:
2	chr2:183895298..183904606-chr2:183986062..183992067,16	K562	blood:
3	chr2:183856353..183858960-chr2:183895348..183897886,2	K562	blood:
4	chr2:183891999..183897694-chr2:183897904..183904092,6	MCF-7	breast:
5	chr2:183866930..183869323-chr2:183893971..183896366,2	K562	blood:

Variant related genes	Relation type
ENSG00000163002	Chromatin interaction
ENSG00000061676	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1561369	1.00[AFR][1000 genomes]
rs17265824	1.00[AFR][1000 genomes]
rs17265859	1.00[AFR][1000 genomes]
rs17265866	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17265894	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2675073	0.87[CEU][hapmap]
rs41270217	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72900703	1.00[AFR][1000 genomes]
rs7595898	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1005281	chr2:183803173-184093877	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv875485	chr2:183827018-184195265	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1010799	chr2:183855680-184244721	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv536072	chr2:183855680-184244721	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1003519	chr2:183885544-184015868	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17703779	NCKAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183846000-183902000	Weak transcription	Lung	lung
2	chr2:183854000-183898800	Weak transcription	Fetal Brain Male	brain
3	chr2:183859600-183899400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:183875200-183896200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:183875200-183896600	Weak transcription	Hela-S3	cervix
6	chr2:183875400-183897000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:183875400-183899600	Weak transcription	HSMMtube	muscle
8	chr2:183878800-183902000	Weak transcription	Esophagus	oesophagus
9	chr2:183879200-183900200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:183879600-183897600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:183880200-183900800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr2:183881800-183897800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:183882600-183896400	Weak transcription	Fetal Brain Female	brain
14	chr2:183883400-183896400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:183886400-183896400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:183886600-183897600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr2:183886600-183898800	Weak transcription	Fetal Intestine Small	intestine
18	chr2:183886600-183899600	Weak transcription	NH-A	brain
19	chr2:183886600-183900600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr2:183886800-183900600	Weak transcription	Fetal Stomach	stomach
21	chr2:183887200-183896200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:183887600-183899200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:183887800-183897600	Weak transcription	HSMM	muscle
24	chr2:183887800-183898600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:183887800-183899800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr2:183888000-183896800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:183888600-183899000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr2:183888800-183896400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:183888800-183897000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:183888800-183899000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:183889200-183897200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr2:183889800-183896400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:183889800-183897600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:183889800-183897800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:183889800-183899600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:183889800-183900600	Weak transcription	Fetal Lung	lung
37	chr2:183889800-183902000	Weak transcription	Gastric	stomach
38	chr2:183890000-183897800	Weak transcription	Osteobl	bone
39	chr2:183890800-183896200	Weak transcription	NHDF-Ad	bronchial
40	chr2:183891000-183899200	Weak transcription	NHLF	lung
41	chr2:183891200-183900600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:183891400-183899600	Weak transcription	Fetal Intestine Large	intestine
43	chr2:183891400-183901800	Weak transcription	Small Intestine	intestine
44	chr2:183891600-183896000	Weak transcription	Stomach Mucosa	stomach
45	chr2:183891600-183896200	Weak transcription	Liver	Liver
46	chr2:183892000-183897000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr2:183892200-183896200	Weak transcription	HepG2	liver
48	chr2:183893200-183897600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:183894000-183896400	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr2:183894000-183900000	Enhancers	Duodenum Smooth Muscle	Duodenum

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