Variant report

Variant	rs10772999
Chromosome Location	chr12:123728230-123728231
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123728216-123728769	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:123728167-123728649	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123721738..123724481-chr12:123725404..123728310,3	K562	blood:
2	chr12:123715079..123721002-chr12:123721919..123730378,16	K562	blood:

Variant related genes	Relation type
C12orf65	TF binding region
ENSG00000051825	Chromatin interaction
ENSG00000130921	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10732573	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10734901	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10744150	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10744151	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10772997	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10772998	0.82[EUR][1000 genomes]
rs10773002	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10846487	0.81[EUR][1000 genomes]
rs11057189	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11057202	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11057204	0.83[EUR][1000 genomes]
rs11057205	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057206	0.82[EUR][1000 genomes]
rs11057207	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057209	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11057210	0.81[EUR][1000 genomes]
rs11532322	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11554169	0.90[ASN][1000 genomes]
rs12817892	0.81[EUR][1000 genomes]
rs12818067	0.81[EUR][1000 genomes]
rs12829456	0.81[EUR][1000 genomes]
rs1568427	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1568428	0.81[ASN][1000 genomes]
rs1609520	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1615350	0.80[EUR][1000 genomes]
rs1716170	0.81[EUR][1000 genomes]
rs1716171	0.81[EUR][1000 genomes]
rs1727319	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1727331	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1727332	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1727334	0.81[EUR][1000 genomes]
rs1879379	0.84[ASN][1000 genomes]
rs1969355	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1980251	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2090764	0.94[ASN][1000 genomes]
rs2102949	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2280424	0.97[ASN][1000 genomes]
rs2337630	0.83[ASN][1000 genomes]
rs2337631	0.83[ASN][1000 genomes]
rs28362667	0.90[ASN][1000 genomes]
rs28362669	0.88[ASN][1000 genomes]
rs2851443	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2851447	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34341465	0.81[EUR][1000 genomes]
rs34841857	0.84[ASN][1000 genomes]
rs36121382	0.85[ASN][1000 genomes]
rs3759111	0.84[ASN][1000 genomes]
rs3759114	0.87[ASN][1000 genomes]
rs4460848	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4474478	0.98[ASN][1000 genomes]
rs4474479	0.98[ASN][1000 genomes]
rs4594040	0.98[ASN][1000 genomes]
rs4759372	0.91[ASN][1000 genomes]
rs4759406	0.82[ASN][1000 genomes]
rs4759407	0.84[ASN][1000 genomes]
rs4759408	0.91[ASN][1000 genomes]
rs4759409	0.80[EUR][1000 genomes]
rs4759411	0.90[ASN][1000 genomes]
rs4759413	0.89[ASN][1000 genomes]
rs4759414	0.89[ASN][1000 genomes]
rs4759418	0.92[ASN][1000 genomes]
rs57676984	0.91[ASN][1000 genomes]
rs58809476	0.81[EUR][1000 genomes]
rs60077920	0.91[ASN][1000 genomes]
rs60254089	0.88[ASN][1000 genomes]
rs60296110	0.82[ASN][1000 genomes]
rs61231969	0.92[ASN][1000 genomes]
rs61519741	1.00[ASN][1000 genomes]
rs7137286	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139321	0.81[ASN][1000 genomes]
rs7304782	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7313483	0.81[EUR][1000 genomes]
rs73231928	0.81[ASN][1000 genomes]
rs941305	0.81[EUR][1000 genomes]
rs941306	0.81[EUR][1000 genomes]
rs9795522	0.82[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	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10772999	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs10772999	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs10772999	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs10772999	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs10772999	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs10772999	RP11-282O18.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123718800-123728400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:123718800-123728400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:123718800-123733000	Weak transcription	Esophagus	oesophagus
4	chr12:123718800-123733800	Weak transcription	Aorta	Aorta
5	chr12:123718800-123739600	Weak transcription	Fetal Kidney	kidney
6	chr12:123719000-123728400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:123719000-123731600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:123719000-123732600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr12:123719000-123735000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:123719200-123733000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:123719200-123735200	Weak transcription	Ovary	ovary
12	chr12:123719600-123734200	Weak transcription	Colonic Mucosa	Colon
13	chr12:123719600-123738400	Weak transcription	NH-A	brain
14	chr12:123719800-123728800	Strong transcription	Fetal Stomach	stomach
15	chr12:123719800-123733600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:123719800-123733600	Weak transcription	Spleen	Spleen
17	chr12:123719800-123733800	Weak transcription	Fetal Intestine Large	intestine
18	chr12:123720000-123732800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:123720000-123736000	Weak transcription	Gastric	stomach
20	chr12:123720000-123738000	Weak transcription	Small Intestine	intestine
21	chr12:123720200-123735200	Weak transcription	Pancreas	Pancrea
22	chr12:123720600-123733000	Weak transcription	Fetal Brain Female	brain
23	chr12:123721000-123733800	Weak transcription	Lung	lung
24	chr12:123721600-123735200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:123722800-123733600	Weak transcription	Osteobl	bone
26	chr12:123723000-123733000	Weak transcription	Dnd41	blood
27	chr12:123723200-123729400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:123723200-123733000	Weak transcription	NHLF	lung
29	chr12:123723400-123735000	Weak transcription	Stomach Mucosa	stomach
30	chr12:123723600-123733000	Weak transcription	Primary B cells from cord blood	blood
31	chr12:123724400-123733000	Weak transcription	HMEC	breast
32	chr12:123724600-123735200	Weak transcription	Placenta	Placenta
33	chr12:123725200-123738000	Weak transcription	HSMM	muscle
34	chr12:123725800-123746400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr12:123726400-123728800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr12:123726600-123729200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:123726600-123733000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr12:123726600-123735200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr12:123726800-123728400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
40	chr12:123727000-123733000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr12:123727000-123733000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:123727000-123735000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr12:123727200-123728600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr12:123727200-123728800	Enhancers	Primary T cells from cord blood	blood
45	chr12:123727200-123732600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr12:123727200-123732600	Weak transcription	Liver	Liver
47	chr12:123727200-123733000	Weak transcription	Brain Germinal Matrix	brain
48	chr12:123727200-123735000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:123727200-123735000	Weak transcription	Brain Hippocampus Middle	brain
50	chr12:123727200-123735000	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links