Variant report

Variant	rs12997656
Chromosome Location	chr2:55394166-55394167
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55291031..55292984-chr2:55393872..55396324,2	K562	blood:
2	chr2:55389326..55391363-chr2:55393207..55395340,2	K562	blood:
3	chr2:55275064..55280479-chr2:55390367..55395295,9	MCF-7	breast:
4	chr2:55274543..55277923-chr2:55387934..55394752,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10167669	0.83[ASN][1000 genomes]
rs10193022	0.81[ASN][1000 genomes]
rs11692206	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12615414	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12988617	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13021163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34348115	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34511570	0.84[EUR][1000 genomes]
rs56039135	0.83[EUR][1000 genomes]
rs71414550	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7580936	0.80[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12997656	CLHC1	cis	Thyroid	GTEx
rs12997656	CLHC1	cis	Muscle Skeletal	GTEx
rs12997656	CLHC1	cis	Nerve Tibial	GTEx
rs12997656	CLHC1	cis	Artery Tibial	GTEx
rs12997656	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs12997656	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL
rs12997656	CLHC1	cis	Esophagus Muscularis	GTEx
rs12997656	CLHC1	cis	Artery Aorta	GTEx
rs12997656	CLHC1	cis	Adipose Subcutaneous	GTEx
rs12997656	CLHC1	cis	lung	GTEx
rs12997656	CLHC1	cis	Whole Blood	GTEx
rs12997656	C2orf63	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55383600-55395600	Enhancers	Pancreas	Pancrea
2	chr2:55386000-55395000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:55386800-55416600	Weak transcription	Esophagus	oesophagus
4	chr2:55387400-55395600	Enhancers	Lung	lung
5	chr2:55387600-55395000	Weak transcription	Psoas Muscle	Psoas
6	chr2:55388000-55395200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:55388800-55395000	Weak transcription	Left Ventricle	heart
8	chr2:55389000-55394800	Enhancers	Brain Cingulate Gyrus	brain
9	chr2:55389000-55394800	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr2:55389200-55394800	Enhancers	Brain Anterior Caudate	brain
11	chr2:55389200-55397400	Enhancers	NHLF	lung
12	chr2:55389400-55394800	Enhancers	Brain Hippocampus Middle	brain
13	chr2:55389400-55395200	Weak transcription	NHEK	skin
14	chr2:55389800-55394600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:55389800-55395000	Weak transcription	Brain Germinal Matrix	brain
16	chr2:55389800-55396000	Enhancers	Fetal Muscle Leg	muscle
17	chr2:55390000-55395600	Enhancers	Ovary	ovary
18	chr2:55390200-55394800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:55390200-55395200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:55390400-55394800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:55390400-55395000	Weak transcription	Fetal Thymus	thymus
22	chr2:55390400-55395200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:55390400-55395600	Enhancers	Right Atrium	heart
24	chr2:55390600-55395800	Enhancers	K562	blood
25	chr2:55390800-55394600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:55391000-55394800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr2:55391000-55395400	Weak transcription	Spleen	Spleen
28	chr2:55391000-55397000	Enhancers	Brain Angular Gyrus	brain
29	chr2:55391200-55394600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:55391200-55394600	Weak transcription	Fetal Stomach	stomach
31	chr2:55391200-55395000	Enhancers	Brain Substantia Nigra	brain
32	chr2:55391200-55397000	Enhancers	NHDF-Ad	bronchial
33	chr2:55391400-55394600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:55391400-55394600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:55391400-55395000	Weak transcription	Aorta	Aorta
36	chr2:55391400-55395800	Enhancers	Stomach Mucosa	stomach
37	chr2:55391600-55394800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:55391800-55394200	Enhancers	Fetal Intestine Large	intestine
39	chr2:55392000-55394600	Weak transcription	Fetal Lung	lung
40	chr2:55392000-55394800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr2:55392000-55395000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr2:55392000-55395400	Weak transcription	Fetal Brain Male	brain
43	chr2:55392000-55397400	Enhancers	HSMM	muscle
44	chr2:55392200-55394600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr2:55392200-55394800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr2:55392200-55395000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:55392200-55395800	Enhancers	Adipose Nuclei	Adipose
48	chr2:55392400-55394600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:55392400-55394800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr2:55392400-55395000	Weak transcription	H9 Cell Line	embryonic stem cell

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