Variant report

Variant	rs1476607
Chromosome Location	chr12:48524804-48524805
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48512350..48514595-chr12:48524789..48526462,2	MCF-7	breast:
2	chr12:48518519..48521118-chr12:48522824..48524892,2	MCF-7	breast:
3	chr12:48523386..48526206-chr12:48526341..48529296,3	K562	blood:
4	chr12:48524259..48525822-chr12:48531923..48533830,2	MCF-7	breast:
5	chr12:48515142..48518168-chr12:48522729..48524957,3	MCF-7	breast:
6	chr12:48518849..48522822-chr12:48523598..48527122,4	K562	blood:
7	chr12:48511904..48514441-chr12:48524039..48526074,2	MCF-7	breast:
8	chr12:48524575..48527145-chr12:48529433..48531470,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000152556	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10161358	0.85[EUR][1000 genomes]
rs10875716	0.82[ASW][hapmap];0.81[CEU][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap]
rs10875718	0.80[CEU][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs10875719	0.80[CEU][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs10875743	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10875749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs1107654	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap]
rs11168338	0.83[LWK][hapmap]
rs11168351	0.82[ASW][hapmap];0.81[CEU][hapmap]
rs11168408	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11168411	1.00[LWK][hapmap]
rs11168428	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]
rs11168437	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]
rs11168441	1.00[CHB][hapmap]
rs11168460	1.00[CHB][hapmap]
rs12099462	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12228750	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs12816820	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs17122498	1.00[CHB][hapmap]
rs2051851	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.91[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]
rs3997	0.92[CEU][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760612	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs4760679	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580650	0.92[CEU][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs6580652	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580654	0.87[EUR][1000 genomes]
rs7139330	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295580	0.82[EUR][1000 genomes]
rs7297824	1.00[CHB][hapmap]
rs7301003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[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[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap]
rs7971880	0.81[CEU][hapmap];0.92[MEX][hapmap]
rs7975632	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8716	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];0.99[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];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9971924	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][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	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1476607	PRPF40B	cis	parietal	SCAN
rs1476607	PFKM	cis	parietal	SCAN
rs1476607	OR6C70	trans	parietal	SCAN
rs1476607	C12orf68	cis	cerebellum	SCAN
rs1476607	H1FNT	cis	Muscle Skeletal	GTEx
rs1476607	RPAP3	cis	cerebellum	SCAN
rs1476607	RP1-228P16.1	cis	Artery Tibial	GTEx
rs1476607	DDX23	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48513400-48526600	Weak transcription	Spleen	Spleen
2	chr12:48513600-48526400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:48513600-48527000	Weak transcription	Pancreas	Pancrea
4	chr12:48513800-48525000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:48513800-48525000	Weak transcription	Lung	lung
6	chr12:48513800-48525800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:48513800-48526000	Weak transcription	Colonic Mucosa	Colon
8	chr12:48513800-48526400	Weak transcription	Gastric	stomach
9	chr12:48513800-48526600	Weak transcription	Thymus	Thymus
10	chr12:48513800-48526800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:48514000-48525000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:48514000-48525000	Weak transcription	Brain Substantia Nigra	brain
13	chr12:48514000-48525000	Weak transcription	Esophagus	oesophagus
14	chr12:48514000-48525600	Weak transcription	Placenta	Placenta
15	chr12:48514000-48526400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr12:48514000-48526600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:48514000-48526600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:48514000-48536600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr12:48514000-48537200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:48514200-48527000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr12:48514400-48525400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr12:48514400-48526400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:48514600-48526200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:48514800-48526000	Weak transcription	Brain Hippocampus Middle	brain
25	chr12:48515600-48535600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr12:48515800-48535600	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:48515800-48545600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:48516200-48529600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr12:48516200-48545400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:48516200-48547200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:48516400-48529400	Strong transcription	Ovary	ovary
32	chr12:48516400-48529600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:48516400-48535600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:48516400-48535800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:48516400-48542000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:48516400-48545000	Strong transcription	GM12878-XiMat	blood
37	chr12:48516400-48545400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:48516400-48545800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:48516400-48547200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:48516400-48547200	Strong transcription	Stomach Smooth Muscle	stomach
41	chr12:48516400-48547800	Strong transcription	Fetal Stomach	stomach
42	chr12:48516600-48525000	Weak transcription	Fetal Intestine Small	intestine
43	chr12:48516600-48525000	Weak transcription	Right Atrium	heart
44	chr12:48516600-48527800	Weak transcription	Small Intestine	intestine
45	chr12:48516600-48536600	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr12:48516600-48543200	Weak transcription	Stomach Mucosa	stomach
47	chr12:48516600-48545400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:48516600-48545600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:48516800-48529400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr12:48516800-48530400	Strong transcription	Osteobl	bone

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