Variant report

Variant	rs12298826
Chromosome Location	chr12:123829028-123829029
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123827417..123830672-chr12:123833003..123836389,3	K562	blood:
2	chr12:123823663..123826008-chr12:123828562..123831019,3	K562	blood:
3	chr12:123828575..123831228-chr12:123848385..123850179,2	K562	blood:
4	chr12:123824508..123827696-chr12:123828815..123831439,3	K562	blood:
5	chr12:123755684..123757295-chr12:123828561..123830250,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256092	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000207189	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1051431	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1060105	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs10772998	0.89[CEU][hapmap]
rs10773002	0.81[GIH][hapmap]
rs10773008	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10846486	0.94[CEU][hapmap]
rs10846515	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11057192	0.89[CEU][hapmap];0.97[TSI][hapmap]
rs11057270	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11830103	0.92[CEU][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12299125	0.84[EUR][1000 genomes]
rs12304248	0.94[CEU][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12316131	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12322888	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12817892	0.91[CEU][hapmap]
rs12821431	0.90[EUR][1000 genomes]
rs1402274	0.94[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap]
rs1402275	0.93[GIH][hapmap]
rs1533703	0.88[CEU][hapmap]
rs1568427	0.85[GIH][hapmap]
rs1569068	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1609520	0.85[GIH][hapmap]
rs1615350	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs1716157	0.94[CEU][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap]
rs1716160	0.94[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs1716164	0.94[CEU][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap]
rs1716165	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1716167	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1716168	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1716170	0.94[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs1716171	0.94[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs1716175	0.94[CEU][hapmap]
rs1716176	0.94[CEU][hapmap]
rs1716177	0.94[CEU][hapmap]
rs1727296	0.94[CEU][hapmap]
rs1727302	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs1727306	0.94[CEU][hapmap]
rs1727309	0.94[CEU][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap]
rs1727313	0.94[CEU][hapmap];1.00[TSI][hapmap]
rs1727315	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1727320	0.94[CEU][hapmap]
rs1727323	0.94[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs1727324	0.94[CEU][hapmap]
rs1727325	0.94[CEU][hapmap]
rs1727331	0.85[GIH][hapmap]
rs1727334	0.86[CEU][hapmap]
rs1790095	0.94[CEU][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap]
rs1790098	0.94[CEU][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap]
rs1790100	0.94[CEU][hapmap]
rs1790108	0.94[CEU][hapmap];0.97[TSI][hapmap]
rs1790123	0.94[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap]
rs1790131	0.94[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs1879380	0.94[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs1969354	0.89[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs1980252	0.89[CEU][hapmap]
rs2049114	0.94[CEU][hapmap]
rs2337934	0.89[CEU][hapmap];0.93[GIH][hapmap];0.94[TSI][hapmap]
rs2682434	0.94[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs2695478	0.94[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap]
rs28406193	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs28458312	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs28472704	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs2851447	0.82[CEU][hapmap]
rs28569885	0.94[GIH][hapmap];0.91[TSI][hapmap]
rs28582096	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28583837	0.84[EUR][1000 genomes]
rs28592876	0.84[EUR][1000 genomes]
rs28625019	0.82[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap]
rs28636834	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs28675824	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28683528	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28706696	0.82[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap]
rs28809230	0.82[EUR][1000 genomes]
rs34997336	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4372492	0.94[CEU][hapmap]
rs4460848	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs4759371	0.89[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs4759409	0.89[CEU][hapmap]
rs4759415	0.89[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs4759420	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4930718	0.91[GIH][hapmap];0.88[TSI][hapmap]
rs6488868	0.88[ASW][hapmap]
rs67624109	0.99[EUR][1000 genomes]
rs71444571	0.80[EUR][1000 genomes]
rs7304782	0.85[GIH][hapmap]
rs7306755	0.81[EUR][1000 genomes]
rs7313483	0.89[CEU][hapmap]
rs7485502	0.84[EUR][1000 genomes]
rs7953929	0.94[CEU][hapmap];0.93[GIH][hapmap]
rs7955457	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7980687	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs884548	0.94[CEU][hapmap]
rs9300255	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs941305	0.94[CEU][hapmap]
rs941306	0.94[CEU][hapmap]
rs9739070	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12298826	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs12298826	CDK2AP1	cis	Adipose Subcutaneous	GTEx
rs12298826	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs12298826	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs12298826	RP11-282O18.3	cis	Adipose Subcutaneous	GTEx
rs12298826	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs12298826	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs12298826	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs12298826	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123772400-123847800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:123773000-123835200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:123773200-123830600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr12:123773200-123834200	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr12:123773200-123835000	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr12:123773200-123835000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:123773200-123838000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:123773400-123835000	Strong transcription	Fetal Thymus	thymus
9	chr12:123773400-123835400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:123773400-123837200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:123773600-123830800	Strong transcription	Placenta	Placenta
12	chr12:123773600-123835200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr12:123773600-123835400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:123773800-123834800	Strong transcription	Duodenum Mucosa	Duodenum
15	chr12:123773800-123837200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:123773800-123837400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:123774000-123835000	Strong transcription	Fetal Muscle Trunk	muscle
18	chr12:123774000-123835200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr12:123774000-123835400	Strong transcription	Dnd41	blood
20	chr12:123775600-123835400	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:123776200-123830600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr12:123776400-123835000	Strong transcription	Thymus	Thymus
23	chr12:123776600-123834400	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr12:123777000-123835400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr12:123777600-123834800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:123780000-123830600	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:123785600-123830800	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr12:123785600-123835000	Strong transcription	Fetal Muscle Leg	muscle
29	chr12:123790200-123835000	Strong transcription	Fetal Intestine Large	intestine
30	chr12:123799800-123833000	Strong transcription	Stomach Smooth Muscle	stomach
31	chr12:123805000-123834000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr12:123805200-123835200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:123807600-123845200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr12:123809400-123831000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:123811200-123830400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:123812200-123835200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:123813800-123835600	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:123815200-123835600	Strong transcription	Fetal Intestine Small	intestine
39	chr12:123815200-123837200	Strong transcription	Fetal Stomach	stomach
40	chr12:123815400-123835000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr12:123815600-123842000	Weak transcription	Psoas Muscle	Psoas
42	chr12:123815800-123830000	Weak transcription	Small Intestine	intestine
43	chr12:123816000-123838400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr12:123816000-123847400	Weak transcription	Stomach Mucosa	stomach
45	chr12:123817400-123830600	Strong transcription	Osteobl	bone
46	chr12:123817600-123834200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:123817800-123831000	Strong transcription	Left Ventricle	heart
48	chr12:123817800-123834800	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr12:123818200-123832800	Strong transcription	HepG2	liver
50	chr12:123819400-123830800	Strong transcription	Primary T cells from cord blood	blood

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