Variant report

Variant	rs17125088
Chromosome Location	chr12:51326702-51326703
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51325611..51327602-chr12:51338374..51340609,2	K562	blood:
2	chr12:51322696..51325064-chr12:51325952..51327620,2	K562	blood:
3	chr12:51325288..51327339-chr12:51334095..51336282,2	K562	blood:
4	chr12:51325095..51327824-chr12:51330132..51332828,3	K562	blood:
5	chr12:51320296..51325528-chr12:51326081..51329757,6	K562	blood:
6	chr12:51325095..51328187-chr12:51330132..51332748,3	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1079521	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11169627	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169632	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12304878	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12304921	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12305170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12306808	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12310511	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12315928	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12316856	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12317171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12318464	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12582592	0.82[JPT][hapmap]
rs17122760	0.88[CEU][hapmap];0.95[CHB][hapmap]
rs17125116	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17125286	0.95[CHB][hapmap]
rs17125346	0.95[CHB][hapmap]
rs17125375	0.81[JPT][hapmap]
rs17125401	0.82[JPT][hapmap]
rs224446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs224454	0.83[EUR][1000 genomes]
rs224568	1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs224587	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2269684	0.83[EUR][1000 genomes]
rs2269685	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2269686	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs453313	0.83[EUR][1000 genomes]
rs4768941	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4768942	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4768943	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4768944	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4768945	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4768948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56087503	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56303785	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56402416	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58999537	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59546367	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61577980	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66518563	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66744607	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67106267	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67420027	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67646958	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67654320	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67669227	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73090629	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73090631	0.97[EUR][1000 genomes]
rs73090647	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73090649	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73090666	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73092531	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73092537	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73295896	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73310004	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73310020	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7397068	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7973904	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17125088	TFCP2	cis	multi-tissue	Pritchard
rs17125088	KRT1	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51319400-51346200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:51320200-51330600	Weak transcription	Primary T cells from cord blood	blood
3	chr12:51320400-51328600	Weak transcription	HSMM	muscle
4	chr12:51320600-51327400	Weak transcription	Placenta	Placenta
5	chr12:51320600-51328200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:51322200-51327200	Weak transcription	Fetal Heart	heart
7	chr12:51322200-51327200	Weak transcription	NHDF-Ad	bronchial
8	chr12:51322200-51327400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:51322200-51327400	Weak transcription	HSMMtube	muscle
10	chr12:51322200-51332600	Weak transcription	Fetal Kidney	kidney
11	chr12:51322400-51327200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:51322400-51327200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:51322400-51327200	Weak transcription	Esophagus	oesophagus
14	chr12:51322400-51327600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr12:51322400-51327800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:51322400-51329000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:51322600-51326800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:51322600-51327200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:51322800-51326800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:51322800-51327600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:51322800-51328200	Weak transcription	NHEK	skin
22	chr12:51322800-51331800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:51323000-51327200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:51323000-51327200	Weak transcription	Right Atrium	heart
25	chr12:51323000-51327800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:51323000-51331000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:51323000-51377200	Weak transcription	Aorta	Aorta
28	chr12:51323200-51328000	Weak transcription	NHLF	lung
29	chr12:51323400-51327200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:51323400-51327200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr12:51323400-51327600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:51323400-51327600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr12:51323400-51330000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr12:51323400-51330800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr12:51323400-51330800	Weak transcription	Brain Germinal Matrix	brain
36	chr12:51323400-51330800	Weak transcription	Fetal Brain Female	brain
37	chr12:51323600-51327200	Weak transcription	Brain Anterior Caudate	brain
38	chr12:51323600-51328200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:51323600-51328400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr12:51323800-51328000	Strong transcription	Stomach Smooth Muscle	stomach
41	chr12:51324000-51328000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
42	chr12:51324200-51331200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr12:51324400-51331200	Enhancers	Stomach Mucosa	stomach
44	chr12:51324600-51327200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr12:51324600-51327200	Weak transcription	Left Ventricle	heart
46	chr12:51324600-51327200	Weak transcription	Pancreas	Pancrea
47	chr12:51324600-51327200	Weak transcription	Psoas Muscle	Psoas
48	chr12:51324600-51327200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr12:51324600-51327400	Weak transcription	Gastric	stomach
50	chr12:51324600-51327400	Weak transcription	Spleen	Spleen

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