Variant report

Variant	rs12950335
Chromosome Location	chr17:38215314-38215315
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38186192..38189163-chr17:38215135..38216733,2	MCF-7	breast:
2	chr17:38214747..38216418-chr17:38217920..38219694,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000126351	Chromatin interaction
ENSG00000008838	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1042658	0.84[ASN][1000 genomes]
rs1045929	0.80[ASN][1000 genomes]
rs11078934	0.93[ASN][1000 genomes]
rs11871747	0.83[ASN][1000 genomes]
rs2227315	0.84[ASN][1000 genomes]
rs2227322	0.84[ASN][1000 genomes]
rs2227336	0.84[ASN][1000 genomes]
rs3213762	0.84[ASN][1000 genomes]
rs3884477	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3935280	0.92[ASN][1000 genomes]
rs3936197	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4794824	0.84[ASN][1000 genomes]
rs57065891	0.84[ASN][1000 genomes]
rs59925331	0.84[ASN][1000 genomes]
rs62065216	0.81[EUR][1000 genomes]
rs709591	0.84[ASN][1000 genomes]
rs709592	0.84[ASN][1000 genomes]
rs7208815	0.82[ASN][1000 genomes]
rs7209755	0.84[ASN][1000 genomes]
rs7214085	0.84[ASN][1000 genomes]
rs7502514	0.92[ASN][1000 genomes]
rs7502912	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7503555	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8065443	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8066846	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8078692	1.00[ASN][1000 genomes]
rs868150	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9303283	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9303284	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12950335	GSDMA	cis	lung	GTEx
rs12950335	MED24	cis	Esophagus Muscularis	GTEx
rs12950335	MED24	cis	Artery Tibial	GTEx
rs12950335	GSDMA	cis	Adipose Subcutaneous	GTEx
rs12950335	MED24	cis	Nerve Tibial	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38211000-38217400	Weak transcription	Gastric	stomach
2	chr17:38211200-38217200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:38211200-38217200	Weak transcription	Esophagus	oesophagus
4	chr17:38211200-38217200	Weak transcription	Pancreas	Pancrea
5	chr17:38211200-38217600	Weak transcription	Colonic Mucosa	Colon
6	chr17:38211200-38218600	Weak transcription	Left Ventricle	heart
7	chr17:38211200-38218600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr17:38211400-38215600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr17:38211400-38216000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr17:38211400-38216200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr17:38211400-38217400	Weak transcription	Brain Anterior Caudate	brain
12	chr17:38211400-38217600	Weak transcription	Fetal Intestine Large	intestine
13	chr17:38211400-38218000	Weak transcription	Brain Hippocampus Middle	brain
14	chr17:38211400-38218200	Weak transcription	Primary T cells from cord blood	blood
15	chr17:38211400-38218200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr17:38211400-38218200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr17:38211400-38218200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr17:38211400-38218200	Weak transcription	Hela-S3	cervix
19	chr17:38211400-38218400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr17:38211400-38218400	Weak transcription	Brain Substantia Nigra	brain
21	chr17:38211400-38218400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr17:38213000-38217200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr17:38213400-38216400	Weak transcription	Brain Germinal Matrix	brain
24	chr17:38214000-38215400	Enhancers	Fetal Muscle Leg	muscle
25	chr17:38214000-38217400	Weak transcription	Brain Angular Gyrus	brain
26	chr17:38214200-38215800	Enhancers	Colon Smooth Muscle	Colon
27	chr17:38214400-38215400	Enhancers	Duodenum Mucosa	Duodenum
28	chr17:38214400-38215400	Enhancers	Fetal Lung	lung
29	chr17:38214600-38215400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr17:38214600-38217400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr17:38214600-38217400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr17:38214600-38217400	Weak transcription	Spleen	Spleen
33	chr17:38214600-38218000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr17:38214600-38218200	Weak transcription	Right Ventricle	heart
35	chr17:38214800-38215400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr17:38214800-38215800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr17:38214800-38215800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr17:38214800-38216000	Weak transcription	Fetal Brain Male	brain
39	chr17:38214800-38216200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr17:38214800-38216200	Weak transcription	Fetal Brain Female	brain
41	chr17:38214800-38216200	Bivalent Enhancer	HepG2	liver
42	chr17:38214800-38217200	Weak transcription	Fetal Thymus	thymus
43	chr17:38214800-38217400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr17:38214800-38217400	Weak transcription	Fetal Intestine Small	intestine
45	chr17:38214800-38217400	Weak transcription	K562	blood
46	chr17:38214800-38218400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr17:38214800-38218600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr17:38214800-38218600	Weak transcription	HUVEC	blood vessel
49	chr17:38215000-38215400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr17:38215000-38215400	Enhancers	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links