Variant report

Variant	rs11168428
Chromosome Location	chr12:48547128-48547129
allele	C/T
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	chr12:48546925-48547471	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:48546821-48547867	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:48546567-48547561	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:48547069-48547907	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr12:48546842-48547464	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr12:48547014-48547283	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr12:48547046-48547386	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48545842..48549323-chr12:48549562..48552963,3	MCF-7	breast:
2	chr12:48545367..48547255-chr12:48549317..48550994,3	MCF-7	breast:

Variant related genes	Relation type
ASB8	TF binding region
ENSG00000177981	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10161358	0.83[EUR][1000 genomes]
rs10875716	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs10875718	0.80[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap]
rs10875719	0.80[CEU][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap]
rs10875743	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10875749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875753	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1107654	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap]
rs11168351	0.81[CEU][hapmap]
rs11168352	0.80[YRI][hapmap]
rs11168408	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11168437	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11168441	1.00[CHB][hapmap]
rs11168460	1.00[CHB][hapmap]
rs12099462	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12228750	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12300777	0.80[YRI][hapmap]
rs12368659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12816820	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1476607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122498	1.00[CHB][hapmap]
rs2051851	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054905	1.00[CHB][hapmap]
rs2408955	0.89[GIH][hapmap]
rs2450994	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs2634681	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs2634684	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs2732448	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs2732466	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs2732481	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs2732484	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs3997	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760612	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs4760679	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580650	0.89[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs6580652	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580654	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7139330	1.00[CHB][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297824	1.00[CHB][hapmap]
rs7301003	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307566	1.00[CHB][hapmap]
rs7315820	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap]
rs7486941	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap]
rs7487682	0.88[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap]
rs7971880	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs7975632	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8716	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923397	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs973398	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9971924	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11168428	PFKM	cis	parietal	SCAN
rs11168428	OR6C70	trans	parietal	SCAN
rs11168428	PRPF40B	cis	parietal	SCAN
rs11168428	SENP1	cis	parietal	SCAN
rs11168428	RP1-228P16.1	cis	Artery Tibial	GTEx
rs11168428	RPAP3	cis	cerebellum	SCAN
rs11168428	H1FNT	cis	Muscle Skeletal	GTEx
rs11168428	DDX23	cis	parietal	SCAN
rs11168428	C12orf68	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48516200-48547200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:48516400-48547200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:48516400-48547200	Strong transcription	Stomach Smooth Muscle	stomach
4	chr12:48516400-48547800	Strong transcription	Fetal Stomach	stomach
5	chr12:48516800-48547400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:48517600-48547400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:48518600-48547600	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:48519600-48547200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr12:48520800-48547400	Strong transcription	Fetal Brain Female	brain
10	chr12:48523800-48547400	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:48526200-48547600	Strong transcription	Adipose Nuclei	Adipose
12	chr12:48530200-48547600	Strong transcription	Placenta	Placenta
13	chr12:48531000-48547400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:48531000-48547800	Strong transcription	Fetal Muscle Trunk	muscle
15	chr12:48531200-48547400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr12:48531200-48547400	Strong transcription	Duodenum Mucosa	Duodenum
17	chr12:48531200-48547400	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:48531200-48547400	Strong transcription	Fetal Intestine Large	intestine
19	chr12:48531200-48547600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:48531200-48547600	Strong transcription	HMEC	breast
21	chr12:48531200-48547800	Strong transcription	Primary T cells from cord blood	blood
22	chr12:48531200-48547800	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr12:48531200-48547800	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr12:48531200-48548000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:48531400-48547400	Strong transcription	Colonic Mucosa	Colon
26	chr12:48531400-48548000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:48531600-48547200	Strong transcription	Brain Hippocampus Middle	brain
28	chr12:48531600-48547400	Strong transcription	Lung	lung
29	chr12:48531600-48547800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:48532200-48548400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr12:48533000-48547400	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr12:48533000-48547800	Strong transcription	Liver	Liver
33	chr12:48533200-48547600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:48533200-48547800	Strong transcription	Fetal Thymus	thymus
35	chr12:48533600-48547400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:48533600-48548400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr12:48533800-48547800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr12:48534200-48547400	Strong transcription	Brain Cingulate Gyrus	brain
39	chr12:48534200-48548000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr12:48534400-48547600	Strong transcription	Dnd41	blood
41	chr12:48535000-48547800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:48535800-48547400	Strong transcription	Primary B cells from cord blood	blood
43	chr12:48536200-48547400	Strong transcription	Osteobl	bone
44	chr12:48536400-48548200	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr12:48536600-48547800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr12:48536800-48550800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr12:48537800-48550600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr12:48538400-48550200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:48538600-48548600	Strong transcription	Thymus	Thymus
50	chr12:48539200-48547800	Strong transcription	Rectal Smooth Muscle	rectum

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