Variant report

Variant	rs3184122
Chromosome Location	chr12:50570127-50570128
allele	C/T
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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50496386..50497971-chr12:50569174..50571228,2	MCF-7	breast:
2	chr12:50471994..50474538-chr12:50569711..50571544,2	MCF-7	breast:
3	chr12:50468576..50469894-chr12:50568295..50570304,9	MCF-7	breast:
4	chr12:50526217..50526858-chr12:50569299..50570304,3	MCF-7	breast:
5	chr12:50468630..50469759-chr12:50568675..50570193,14	K562	blood:
6	chr12:50479656..50481335-chr12:50569381..50571958,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CERS5-3	chr12:50569572-50570160	NONHSAT028181

No data

Variant related genes	Relation type
ENSG00000110881	Chromatin interaction
ENSG00000167588	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10783338	0.88[CEU][hapmap]
rs10875995	1.00[CHD][hapmap]
rs10876000	0.84[CEU][hapmap]
rs11169270	1.00[CHD][hapmap]
rs11169281	0.84[CEU][hapmap]
rs11169282	0.84[CEU][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap]
rs11169302	0.83[EUR][1000 genomes]
rs12424335	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12817211	0.81[MEX][hapmap]
rs1554844	0.84[CEU][hapmap]
rs17124432	0.84[CEU][hapmap]
rs2302900	0.82[MKK][hapmap]
rs34245511	0.87[EUR][1000 genomes]
rs3741562	0.84[CEU][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap]
rs6580728	0.83[CEU][hapmap]
rs7138945	0.80[CEU][hapmap];0.84[GIH][hapmap]
rs7294618	0.84[CEU][hapmap]
rs7307230	0.84[CEU][hapmap]
rs7308474	0.86[CEU][hapmap]
rs7961065	0.84[CEU][hapmap]
rs7961112	0.84[CEU][hapmap]
rs7964698	0.86[ASN][1000 genomes]
rs7967979	0.83[CEU][hapmap]
rs7968119	0.84[CEU][hapmap]
rs7972465	0.84[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap]
rs9364	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.95[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	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3184122	CERS5	cis	Nerve Tibial	GTEx
rs3184122	LASS5	cis	cerebellum	SCAN
rs3184122	KIAA1463	cis	multi-tissue	Pritchard
rs3184122	ATF1	cis	parietal	SCAN
rs3184122	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs3184122	CELA1	cis	parietal	SCAN
rs3184122	SLC38A1	cis	parietal	SCAN
rs3184122	CERS5	cis	Muscle Skeletal	GTEx
rs3184122	LASS5	cis	parietal	SCAN
rs3184122	SNORA2A	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50561200-50570600	Weak transcription	Aorta	Aorta
2	chr12:50561600-50570600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:50561600-50570800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:50561600-50570800	Weak transcription	Esophagus	oesophagus
5	chr12:50561600-50570800	Weak transcription	Gastric	stomach
6	chr12:50561600-50570800	Weak transcription	Pancreas	Pancrea
7	chr12:50561600-50571200	Weak transcription	Lung	lung
8	chr12:50561600-50571200	Weak transcription	Right Ventricle	heart
9	chr12:50561600-50575200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:50561800-50570400	Weak transcription	Fetal Brain Female	brain
11	chr12:50561800-50570600	Weak transcription	Primary T cells from cord blood	blood
12	chr12:50561800-50570600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr12:50561800-50570800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:50561800-50570800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr12:50561800-50570800	Weak transcription	Brain Angular Gyrus	brain
16	chr12:50561800-50570800	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:50561800-50570800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr12:50561800-50570800	Weak transcription	Ovary	ovary
19	chr12:50561800-50571000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:50561800-50571000	Weak transcription	Colonic Mucosa	Colon
21	chr12:50561800-50571000	Weak transcription	Spleen	Spleen
22	chr12:50561800-50571200	Weak transcription	Brain Germinal Matrix	brain
23	chr12:50561800-50571200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:50561800-50571200	Weak transcription	Left Ventricle	heart
25	chr12:50561800-50571200	Weak transcription	Thymus	Thymus
26	chr12:50561800-50573000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr12:50561800-50574800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr12:50561800-50574800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr12:50561800-50575000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr12:50561800-50582600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr12:50561800-50582600	Weak transcription	Stomach Mucosa	stomach
32	chr12:50562000-50570200	Weak transcription	Liver	Liver
33	chr12:50562000-50570400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:50562000-50570600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr12:50562000-50570600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr12:50562000-50570600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:50562000-50570600	Weak transcription	Fetal Thymus	thymus
38	chr12:50562000-50570800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:50562000-50571000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr12:50562000-50571000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:50562000-50571400	Weak transcription	Fetal Lung	lung
42	chr12:50562000-50576000	Weak transcription	Fetal Heart	heart
43	chr12:50562000-50576400	Weak transcription	A549	lung
44	chr12:50562000-50584800	Weak transcription	K562	blood
45	chr12:50562200-50570400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr12:50562200-50597000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr12:50562400-50570400	Weak transcription	Dnd41	blood
48	chr12:50564400-50570800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr12:50564400-50586200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr12:50564400-50600800	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links