Variant report

Variant	rs28472704
Chromosome Location	chr12:123887369-123887370
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123879282..123881067-chr12:123885695..123887495,2	MCF-7	breast:
2	chr12:123886567..123888097-chr16:33420189..33423186,2	K562	blood:
3	chr12:123886854..123888790-chr12:123919794..123921388,2	MCF-7	breast:
4	chr12:123881479..123883562-chr12:123887318..123890802,3	MCF-7	breast:
5	chr12:123886695..123888203-chr12:123890596..123893402,2	K562	blood:
6	chr12:123873393..123875666-chr12:123886945..123889757,3	K562	blood:
7	chr12:123880916..123883261-chr12:123885627..123887999,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000150977	Chromatin interaction
ENSG00000183955	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1060105	0.89[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs10772998	0.83[CEU][hapmap]
rs10773002	0.81[GIH][hapmap]
rs10846486	0.89[CEU][hapmap]
rs11057192	0.83[CEU][hapmap];0.97[TSI][hapmap]
rs11830103	0.92[CEU][hapmap]
rs12298826	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs12299125	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12304248	0.89[CEU][hapmap]
rs12316131	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs12322888	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs12817892	0.91[CEU][hapmap]
rs1402275	0.93[GIH][hapmap]
rs1533703	0.81[CEU][hapmap]
rs1568427	0.85[GIH][hapmap]
rs1609520	0.85[GIH][hapmap]
rs1716160	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs1716170	0.89[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs1716171	0.89[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs1727320	0.89[CEU][hapmap]
rs1727323	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs1727324	0.89[CEU][hapmap]
rs1727325	0.89[CEU][hapmap]
rs1727331	0.85[GIH][hapmap]
rs1790131	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs1879380	0.89[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs1969354	0.84[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs1980252	0.84[CEU][hapmap]
rs2337934	0.84[CEU][hapmap];0.93[GIH][hapmap];0.94[TSI][hapmap]
rs2682434	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs2695478	0.89[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap]
rs28372579	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28376121	0.82[EUR][1000 genomes]
rs28406193	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28410896	0.80[EUR][1000 genomes]
rs28413626	0.87[EUR][1000 genomes]
rs28458312	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28481863	0.87[EUR][1000 genomes]
rs28569885	0.83[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs28576953	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28582096	0.91[EUR][1000 genomes]
rs28583837	0.92[EUR][1000 genomes]
rs28592876	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28625019	0.89[CEU][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs28636834	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28675824	0.88[EUR][1000 genomes]
rs28676499	0.88[EUR][1000 genomes]
rs28683528	0.86[EUR][1000 genomes]
rs28706696	0.89[CEU][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs28715490	0.89[EUR][1000 genomes]
rs28809230	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28855757	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4372492	0.89[CEU][hapmap]
rs4759371	0.84[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs4759409	0.84[CEU][hapmap]
rs4759415	0.84[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs4930718	0.91[GIH][hapmap];0.88[TSI][hapmap]
rs4930719	0.88[EUR][1000 genomes]
rs6488868	0.82[ASW][hapmap]
rs6576	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7304782	0.85[GIH][hapmap]
rs7313483	0.83[CEU][hapmap]
rs7485502	0.84[EUR][1000 genomes]
rs7953929	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs7980687	0.89[CEU][hapmap]
rs941305	0.89[CEU][hapmap]
rs941306	0.89[CEU][hapmap]

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	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
4	nsv899579	chr12:123843017-123901480	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' 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	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs28472704	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs28472704	CDK2AP1	cis	lymphoblastoid	seeQTL
rs28472704	PITPNM2	cis	cerebellum	SCAN
rs28472704	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs28472704	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs28472704	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs28472704	ANAPC5	cis	parietal	SCAN
rs28472704	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs28472704	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs28472704	LOC283378	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123875200-123894400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:123875600-123894200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:123875600-123895600	Strong transcription	Fetal Thymus	thymus
4	chr12:123875800-123894000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:123876400-123894800	Strong transcription	Fetal Intestine Small	intestine
6	chr12:123876600-123894800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr12:123876800-123887600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:123877400-123889000	Weak transcription	Fetal Heart	heart
9	chr12:123877400-123895600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:123881600-123888200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:123881600-123888400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr12:123881600-123888600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:123881600-123889000	Weak transcription	Fetal Brain Male	brain
14	chr12:123881800-123888800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr12:123881800-123889000	Weak transcription	Fetal Kidney	kidney
16	chr12:123882000-123888600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr12:123882000-123911600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr12:123883200-123895400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:123883800-123894200	Strong transcription	HUVEC	blood vessel
20	chr12:123883800-123895200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:123884000-123887800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:123884000-123888800	Weak transcription	Psoas Muscle	Psoas
23	chr12:123884200-123892800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:123884200-123895200	Strong transcription	Fetal Muscle Trunk	muscle
25	chr12:123886000-123895200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:123886000-123895400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:123886200-123892000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:123886200-123892000	Strong transcription	Primary T cells from cord blood	blood
29	chr12:123886200-123894200	Strong transcription	Fetal Intestine Large	intestine
30	chr12:123886200-123894800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:123886200-123895200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:123886200-123895200	Strong transcription	Fetal Muscle Leg	muscle
33	chr12:123886200-123895200	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr12:123886200-123895200	Strong transcription	Dnd41	blood
35	chr12:123886200-123895400	Strong transcription	Fetal Brain Female	brain
36	chr12:123886400-123887400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr12:123886400-123887400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
38	chr12:123886400-123887400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
39	chr12:123886400-123887400	Genic enhancers	Brain Inferior Temporal Lobe	brain
40	chr12:123886400-123887600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
41	chr12:123886400-123888000	Genic enhancers	Lung	lung
42	chr12:123886400-123888000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr12:123886400-123888200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
44	chr12:123886400-123888800	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr12:123886400-123889200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:123886400-123889200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:123886400-123890200	Strong transcription	Placenta	Placenta
48	chr12:123886400-123891000	Strong transcription	Hela-S3	cervix
49	chr12:123886400-123892200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr12:123886400-123892200	Strong transcription	Brain Germinal Matrix	brain

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