Variant report

Variant	rs57681837
Chromosome Location	chr2:55466229-55466230
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55464660..55467438-chr2:55495235..55498187,2	K562	blood:
2	chr2:55440554..55442948-chr2:55464620..55466638,2	MCF-7	breast:
3	chr17:56707291..56709390-chr2:55464798..55466329,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction
ENSG00000085760	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs17046778	0.95[ASN][1000 genomes]
rs1821832	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2576722	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2920965	0.91[ASN][1000 genomes]
rs57529275	0.89[ASN][1000 genomes]
rs59439819	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59783675	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61109509	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61486882	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6726380	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7349360	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7349405	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][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	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs57681837	CLHC1	cis	Stomach	GTEx
rs57681837	CLHC1	cis	Artery Tibial	GTEx
rs57681837	CLHC1	cis	Esophagus Mucosa	GTEx
rs57681837	CLHC1	cis	Whole Blood	GTEx
rs57681837	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL
rs57681837	CLHC1	cis	Adipose Subcutaneous	GTEx
rs57681837	CLHC1	cis	Thyroid	GTEx
rs57681837	CLHC1	cis	lung	GTEx
rs57681837	CLHC1	cis	Nerve Tibial	GTEx
rs57681837	CLHC1	cis	Artery Aorta	GTEx
rs57681837	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs57681837	CLHC1	cis	Muscle Skeletal	GTEx
rs57681837	CLHC1	cis	Heart Left Ventricle	GTEx
rs57681837	C2orf63	cis	multi-tissue	Pritchard
rs57681837	CLHC1	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55461000-55470200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:55461400-55466600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:55461400-55477600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:55461600-55466600	Strong transcription	Fetal Intestine Large	intestine
5	chr2:55461600-55466600	Strong transcription	HSMMtube	muscle
6	chr2:55461600-55467400	Strong transcription	Adipose Nuclei	Adipose
7	chr2:55461600-55467800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr2:55461600-55469400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:55461600-55471600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:55461600-55477000	Strong transcription	Fetal Muscle Leg	muscle
11	chr2:55461600-55481600	Strong transcription	Fetal Thymus	thymus
12	chr2:55461600-55495400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:55461600-55495400	Weak transcription	Stomach Mucosa	stomach
14	chr2:55461800-55466600	Strong transcription	Primary hematopoietic stem cells	blood
15	chr2:55461800-55467400	Strong transcription	Liver	Liver
16	chr2:55461800-55467400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:55461800-55472400	Weak transcription	Gastric	stomach
18	chr2:55461800-55472400	Weak transcription	Right Ventricle	heart
19	chr2:55461800-55474400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr2:55461800-55493400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:55461800-55495000	Weak transcription	Fetal Brain Male	brain
22	chr2:55462000-55466600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr2:55462000-55467200	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr2:55462000-55467400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:55462000-55467600	Weak transcription	Fetal Intestine Small	intestine
26	chr2:55462000-55472600	Weak transcription	Fetal Heart	heart
27	chr2:55462000-55493200	Strong transcription	Duodenum Mucosa	Duodenum
28	chr2:55462200-55467600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:55462200-55473200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:55462200-55490200	Weak transcription	Small Intestine	intestine
31	chr2:55462400-55466600	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:55462400-55467000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:55462400-55467200	Strong transcription	HMEC	breast
34	chr2:55462400-55467400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:55462400-55476800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:55462400-55476800	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr2:55462600-55466600	Strong transcription	Primary T cells from cord blood	blood
38	chr2:55462600-55466600	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr2:55462600-55467200	Strong transcription	NHDF-Ad	bronchial
40	chr2:55462600-55485800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:55462800-55467800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr2:55463000-55467000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr2:55463000-55467400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:55463000-55467800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:55463000-55477600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:55463000-55480200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr2:55463000-55481000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr2:55463000-55495400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:55463200-55470400	Weak transcription	Colon Smooth Muscle	Colon
50	chr2:55463200-55481000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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