Variant report

Variant	rs12510712
Chromosome Location	chr4:57304571-57304572
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57302424..57305158-chr4:57338707..57340415,2	MCF-7	breast:
2	chr4:57297540..57304787-chr4:57330316..57336934,28	K562	blood:
3	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:
4	chr4:57300392..57305074-chr4:57333261..57337861,17	MCF-7	breast:
5	chr4:57300865..57304829-chr4:57331110..57333239,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270109	Chromatin interaction
ENSG00000174780	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10008223	0.81[ASN][1000 genomes]
rs10013402	0.83[ASN][1000 genomes]
rs10017460	0.82[ASN][1000 genomes]
rs10051	0.83[ASN][1000 genomes]
rs10434444	0.84[ASN][1000 genomes]
rs10434445	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1060472	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11133442	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12501334	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12501502	0.83[EUR][1000 genomes]
rs12503412	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12504291	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12505767	0.80[ASN][1000 genomes]
rs12505939	0.83[ASN][1000 genomes]
rs12508008	0.85[ASN][1000 genomes]
rs12509542	0.85[ASN][1000 genomes]
rs12511770	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12513091	0.91[ASN][1000 genomes]
rs12646890	0.85[ASN][1000 genomes]
rs14211	0.83[ASN][1000 genomes]
rs1474179	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1520026	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1520030	0.80[EUR][1000 genomes]
rs17086696	0.83[ASN][1000 genomes]
rs17086794	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17086832	0.88[ASN][1000 genomes]
rs17086853	0.85[ASN][1000 genomes]
rs1967559	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1983378	0.84[ASN][1000 genomes]
rs2030366	0.84[ASN][1000 genomes]
rs2271923	0.81[EUR][1000 genomes]
rs28510634	0.81[ASN][1000 genomes]
rs28866881	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3796541	0.81[EUR][1000 genomes]
rs4340842	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4346704	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4493603	0.81[EUR][1000 genomes]
rs4618376	0.85[ASN][1000 genomes]
rs4864579	0.83[ASN][1000 genomes]
rs4864580	0.83[ASN][1000 genomes]
rs4864583	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4864585	0.81[ASN][1000 genomes]
rs4865092	0.85[ASN][1000 genomes]
rs4865103	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4865107	0.85[ASN][1000 genomes]
rs4865108	0.83[ASN][1000 genomes]
rs5010012	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55915354	0.83[ASN][1000 genomes]
rs56040009	0.83[ASN][1000 genomes]
rs56099714	0.85[ASN][1000 genomes]
rs56392224	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56887793	0.85[ASN][1000 genomes]
rs58151706	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6554358	0.83[ASN][1000 genomes]
rs66810706	0.81[EUR][1000 genomes]
rs66858948	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs66863699	0.85[ASN][1000 genomes]
rs6820314	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6821301	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6824893	0.82[ASN][1000 genomes]
rs6829250	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6832797	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6834696	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6846895	0.81[EUR][1000 genomes]
rs6849183	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6855041	0.83[EUR][1000 genomes]
rs7664841	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9799864	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12510712	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57295000-57305000	Active TSS	GM12878-XiMat	blood
2	chr4:57298400-57305600	Active TSS	Hela-S3	cervix
3	chr4:57299200-57304800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr4:57299200-57305000	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr4:57299200-57305800	Active TSS	H1 Cell Line	embryonic stem cell
6	chr4:57299200-57305800	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr4:57299200-57305800	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr4:57299400-57304800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:57299400-57305000	Active TSS	K562	blood
10	chr4:57299800-57304800	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr4:57299800-57305600	Active TSS	HepG2	liver
12	chr4:57301600-57304800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr4:57301600-57305200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:57303000-57309000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:57303400-57330800	Weak transcription	Spleen	Spleen
16	chr4:57303800-57308400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:57303800-57326000	Weak transcription	Gastric	stomach
18	chr4:57303800-57331000	Weak transcription	Stomach Mucosa	stomach
19	chr4:57303800-57332000	Weak transcription	Small Intestine	intestine
20	chr4:57304000-57304800	Enhancers	Primary T cells fromperipheralblood	blood
21	chr4:57304000-57305800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:57304000-57306800	Enhancers	Liver	Liver
23	chr4:57304000-57312000	Weak transcription	Left Ventricle	heart
24	chr4:57304000-57315800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:57304000-57330000	Weak transcription	Pancreas	Pancrea
26	chr4:57304000-57330000	Weak transcription	Right Ventricle	heart
27	chr4:57304000-57331800	Weak transcription	Esophagus	oesophagus
28	chr4:57304200-57305000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:57304200-57305200	Weak transcription	Colonic Mucosa	Colon
30	chr4:57304200-57305600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:57304200-57305800	Weak transcription	Brain Angular Gyrus	brain
32	chr4:57304200-57305800	Weak transcription	Fetal Thymus	thymus
33	chr4:57304200-57306400	Weak transcription	Fetal Muscle Leg	muscle
34	chr4:57304200-57307800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr4:57304200-57307800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr4:57304200-57308000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:57304200-57308000	Weak transcription	Placenta	Placenta
38	chr4:57304200-57308200	Weak transcription	Brain Hippocampus Middle	brain
39	chr4:57304200-57314600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr4:57304200-57314800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr4:57304200-57317400	Weak transcription	Thymus	Thymus
42	chr4:57304200-57318800	Weak transcription	Colon Smooth Muscle	Colon
43	chr4:57304200-57319200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr4:57304200-57331800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr4:57304400-57304600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr4:57304400-57304600	Enhancers	Muscle Satellite Cultured Cells	--
47	chr4:57304400-57304600	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr4:57304400-57304600	Enhancers	NH-A	brain
49	chr4:57304400-57304600	Enhancers	NHEK	skin
50	chr4:57304400-57304800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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