Variant report

Variant	rs12601929
Chromosome Location	chr17:38215495-38215496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38210788..38212744-chr17:38215352..38217931,2	MCF-7	breast:
2	chr17:38186192..38189163-chr17:38215135..38216733,2	MCF-7	breast:
3	chr17:38214747..38216418-chr17:38217920..38219694,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000008838	Chromatin interaction
ENSG00000126351	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10445310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11078930	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs11078931	0.81[ASN][1000 genomes]
rs11078935	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11078936	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11654208	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11655264	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs11655655	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11658328	0.91[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs12309	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.81[LWK][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs12451547	0.87[ASN][1000 genomes]
rs12451897	0.84[CEU][hapmap];0.87[ASN][1000 genomes]
rs12453334	0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs12453341	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12453343	0.87[ASN][1000 genomes]
rs12602514	0.81[ASN][1000 genomes]
rs12602854	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12939682	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2227319	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs2227321	0.91[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs2227333	0.87[ASN][1000 genomes]
rs2241244	0.80[ASN][1000 genomes]
rs2241245	0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2270401	0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs2302774	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2302776	0.95[CHB][hapmap];0.81[CHD][hapmap]
rs2302777	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs2305481	0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2305482	0.91[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap]
rs25645	0.87[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.81[LWK][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs34003767	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34342173	0.86[ASN][1000 genomes]
rs34453912	0.86[ASN][1000 genomes]
rs34540281	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34648856	0.82[ASN][1000 genomes]
rs34933056	0.86[ASN][1000 genomes]
rs35272691	0.86[ASN][1000 genomes]
rs35982947	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36071767	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3744245	0.82[ASN][1000 genomes]
rs3859187	0.80[ASN][1000 genomes]
rs3935281	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4065321	0.95[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap]
rs4072639	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66826786	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7502233	0.81[GIH][hapmap];0.88[MEX][hapmap]
rs7502971	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8066582	0.95[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs8070444	0.80[ASN][1000 genomes]
rs8071037	0.80[ASN][1000 genomes]
rs8073254	0.94[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs8075668	0.95[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs9915252	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs9916158	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12601929	MED24	cis	Muscle Skeletal	GTEx
rs12601929	MED24	cis	Artery Tibial	GTEx

Chromatin state (count:63 , 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	chr17:38214000-38217400	Weak transcription	Brain Angular Gyrus	brain
25	chr17:38214200-38215800	Enhancers	Colon Smooth Muscle	Colon
26	chr17:38214600-38217400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr17:38214600-38217400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr17:38214600-38217400	Weak transcription	Spleen	Spleen
29	chr17:38214600-38218000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr17:38214600-38218200	Weak transcription	Right Ventricle	heart
31	chr17:38214800-38215800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr17:38214800-38215800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr17:38214800-38216000	Weak transcription	Fetal Brain Male	brain
34	chr17:38214800-38216200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr17:38214800-38216200	Weak transcription	Fetal Brain Female	brain
36	chr17:38214800-38216200	Bivalent Enhancer	HepG2	liver
37	chr17:38214800-38217200	Weak transcription	Fetal Thymus	thymus
38	chr17:38214800-38217400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr17:38214800-38217400	Weak transcription	Fetal Intestine Small	intestine
40	chr17:38214800-38217400	Weak transcription	K562	blood
41	chr17:38214800-38218400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr17:38214800-38218600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr17:38214800-38218600	Weak transcription	HUVEC	blood vessel
44	chr17:38215000-38216000	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr17:38215000-38217200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr17:38215000-38217200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr17:38215000-38217400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr17:38215000-38218400	Weak transcription	Osteobl	bone
49	chr17:38215000-38218600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr17:38215200-38217400	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links