Variant report

Variant	rs12939682
Chromosome Location	chr17:38194741-38194742
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38186756..38191531-chr17:38192826..38198444,5	K562	blood:
2	chr17:38191841..38193533-chr17:38193734..38195685,2	K562	blood:
3	chr17:38193086..38195422-chr17:38210837..38212580,2	K562	blood:
4	chr17:38193583..38195225-chr17:38212911..38215222,2	K562	blood:
5	chr17:38193120..38197062-chr17:38206698..38210454,3	K562	blood:
6	chr17:38194560..38196821-chr17:38283117..38285170,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000126351	Chromatin interaction
ENSG00000008838	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10445310	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11078930	0.84[ASN][1000 genomes]
rs11078931	0.83[ASN][1000 genomes]
rs11078935	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11078936	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654208	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655264	0.81[ASN][1000 genomes]
rs11655655	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11658328	0.83[ASN][1000 genomes]
rs11867302	0.82[ASN][1000 genomes]
rs12309	0.87[ASN][1000 genomes]
rs12451547	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12451897	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12453334	0.84[ASN][1000 genomes]
rs12453341	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12453343	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12453764	0.81[ASN][1000 genomes]
rs12601929	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12602514	0.83[ASN][1000 genomes]
rs12602854	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12940405	0.81[ASN][1000 genomes]
rs2227319	0.89[ASN][1000 genomes]
rs2227321	0.89[ASN][1000 genomes]
rs2227333	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2241244	0.83[ASN][1000 genomes]
rs2241245	0.83[ASN][1000 genomes]
rs2270401	0.89[ASN][1000 genomes]
rs2302774	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2302777	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2305481	0.83[ASN][1000 genomes]
rs25645	0.88[ASN][1000 genomes]
rs3087852	0.81[ASN][1000 genomes]
rs34003767	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34342173	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34453912	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34540281	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34648856	0.85[ASN][1000 genomes]
rs34933056	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35272691	0.89[ASN][1000 genomes]
rs35982947	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36071767	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3744245	0.85[ASN][1000 genomes]
rs3816472	0.82[ASN][1000 genomes]
rs3859187	0.83[ASN][1000 genomes]
rs3859189	0.81[ASN][1000 genomes]
rs3935281	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4065321	0.82[ASN][1000 genomes]
rs4072639	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4433838	0.82[ASN][1000 genomes]
rs66826786	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7502971	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8066582	0.83[ASN][1000 genomes]
rs8070444	0.83[ASN][1000 genomes]
rs8071037	0.83[ASN][1000 genomes]
rs8073254	0.83[ASN][1000 genomes]
rs8075668	0.81[ASN][1000 genomes]
rs9915252	0.82[ASN][1000 genomes]
rs9916158	0.82[EUR][1000 genomes];0.89[ASN][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	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12939682	MED24	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38176000-38195400	Weak transcription	Right Atrium	heart
2	chr17:38183000-38195600	Strong transcription	Primary T cells from cord blood	blood
3	chr17:38183800-38195000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr17:38183800-38195600	Strong transcription	Fetal Thymus	thymus
5	chr17:38186600-38209800	Weak transcription	Small Intestine	intestine
6	chr17:38188800-38209400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr17:38189600-38195000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr17:38189600-38195000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr17:38189600-38206600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr17:38189600-38209600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr17:38189600-38209600	Weak transcription	Psoas Muscle	Psoas
12	chr17:38189800-38195000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr17:38189800-38195000	Weak transcription	HUVEC	blood vessel
14	chr17:38190600-38209600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr17:38191000-38195400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr17:38191000-38208800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr17:38191400-38201000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr17:38191800-38195000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr17:38191800-38206000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr17:38192000-38194800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr17:38192000-38195000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr17:38192000-38209600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr17:38192200-38195000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr17:38192200-38195000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr17:38192200-38195000	Weak transcription	Right Ventricle	heart
26	chr17:38192200-38195000	Weak transcription	NHDF-Ad	bronchial
27	chr17:38192200-38206600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr17:38192200-38209400	Weak transcription	Fetal Brain Male	brain
29	chr17:38192200-38209600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr17:38192400-38194800	Weak transcription	HSMMtube	muscle
31	chr17:38192400-38195000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr17:38192400-38195000	Weak transcription	Adipose Nuclei	Adipose
33	chr17:38192400-38195000	Weak transcription	Brain Angular Gyrus	brain
34	chr17:38192400-38195000	Weak transcription	Pancreas	Pancrea
35	chr17:38192400-38195000	Weak transcription	HMEC	breast
36	chr17:38192400-38199000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr17:38192400-38209600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr17:38192400-38209600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr17:38192400-38209600	Weak transcription	Colonic Mucosa	Colon
40	chr17:38192400-38209800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr17:38192400-38210000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr17:38192600-38194800	Weak transcription	Fetal Lung	lung
43	chr17:38192600-38195000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr17:38192600-38195000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr17:38192600-38195000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr17:38192600-38195000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr17:38192600-38195000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr17:38192600-38195000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr17:38192600-38195000	Weak transcription	Brain Germinal Matrix	brain
50	chr17:38192600-38195000	Weak transcription	Brain Hippocampus Middle	brain

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