Variant report

Variant	rs56088423
Chromosome Location	chr2:48679498-48679499
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48670330..48672555-chr2:48677413..48681489,3	MCF-7	breast:
2	chr2:48145654..48147755-chr2:48678957..48680778,2	K562	blood:
3	chr2:48666517..48672497-chr2:48674609..48679967,9	MCF-7	breast:
4	chr2:48671508..48673147-chr2:48678922..48681250,2	K562	blood:

Variant related genes	Relation type
ENSG00000272663	Chromatin interaction
ENSG00000162869	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11681187	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55707610	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55952008	0.85[EUR][1000 genomes]
rs56226059	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56088423	CCDC128	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48668600-48682000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:48668800-48679600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr2:48668800-48682400	Weak transcription	Lung	lung
4	chr2:48669000-48680000	Weak transcription	Fetal Stomach	stomach
5	chr2:48669000-48681800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:48669000-48683400	Weak transcription	Right Ventricle	heart
7	chr2:48669200-48698200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:48669400-48685000	Weak transcription	Fetal Brain Female	brain
9	chr2:48669400-48693800	Weak transcription	Hela-S3	cervix
10	chr2:48669600-48694200	Weak transcription	Fetal Brain Male	brain
11	chr2:48670800-48681800	Weak transcription	Gastric	stomach
12	chr2:48670800-48681800	Weak transcription	Spleen	Spleen
13	chr2:48671600-48681800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:48671800-48692400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:48673000-48681600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:48673000-48681800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:48673000-48682000	Weak transcription	Esophagus	oesophagus
18	chr2:48673000-48686800	Weak transcription	Pancreas	Pancrea
19	chr2:48673000-48697400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:48673200-48724000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:48674800-48687000	Weak transcription	Small Intestine	intestine
22	chr2:48675200-48679600	Enhancers	Liver	Liver
23	chr2:48675200-48679600	Enhancers	Placenta Amnion	Placenta Amnion
24	chr2:48675200-48680000	Enhancers	Brain Cingulate Gyrus	brain
25	chr2:48675200-48680400	Enhancers	Brain Anterior Caudate	brain
26	chr2:48675800-48681800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr2:48675800-48687800	Weak transcription	Fetal Kidney	kidney
28	chr2:48676000-48679600	Enhancers	Fetal Heart	heart
29	chr2:48676000-48681800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:48676200-48681000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr2:48676200-48681800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:48676200-48681800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:48676200-48683400	Weak transcription	NHEK	skin
34	chr2:48676200-48686600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:48676200-48692000	Weak transcription	Psoas Muscle	Psoas
36	chr2:48676600-48683200	Weak transcription	HMEC	breast
37	chr2:48676600-48683400	Weak transcription	NHDF-Ad	bronchial
38	chr2:48676800-48685000	Weak transcription	HSMM	muscle
39	chr2:48676800-48688000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr2:48677400-48680000	Strong transcription	Primary B cells from cord blood	blood
41	chr2:48677400-48681800	Weak transcription	Colon Smooth Muscle	Colon
42	chr2:48677400-48683000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:48677600-48681800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr2:48677600-48681800	Weak transcription	Aorta	Aorta
45	chr2:48677600-48681800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:48677600-48683400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:48677600-48685200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:48677600-48686800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr2:48677800-48680400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr2:48677800-48681600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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