Variant report

Variant	rs12450238
Chromosome Location	chr17:16937694-16937695
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16932063..16934977-chr17:16936868..16939174,3	K562	blood:
2	chr17:16931573..16934044-chr17:16934220..16938314,3	MCF-7	breast:

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1047805	0.88[AMR][1000 genomes]
rs10852843	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10852844	0.93[AMR][1000 genomes]
rs10852845	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10852846	0.88[AMR][1000 genomes]
rs11078364	0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11078365	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078366	0.92[ASN][1000 genomes]
rs11078370	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11078371	0.93[AMR][1000 genomes]
rs11078372	0.93[AMR][1000 genomes]
rs11078373	0.88[AMR][1000 genomes]
rs11078375	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1110504	0.92[AMR][1000 genomes]
rs1110505	0.88[AMR][1000 genomes]
rs11651460	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11651938	0.88[AMR][1000 genomes]
rs11651988	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11652079	0.92[AMR][1000 genomes]
rs11652674	0.84[EUR][1000 genomes]
rs11652678	0.88[AMR][1000 genomes]
rs11652756	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11652936	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11654247	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11654360	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11654562	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11658084	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11658904	0.97[ASN][1000 genomes]
rs12450109	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12450213	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12450467	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12451054	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12452303	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12452802	0.92[AMR][1000 genomes]
rs12601325	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12602124	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12602129	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12602867	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16961288	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16961412	0.85[AMR][1000 genomes]
rs2292526	0.84[AMR][1000 genomes]
rs3744125	0.88[AMR][1000 genomes]
rs3744127	0.88[AMR][1000 genomes]
rs3744132	0.88[AMR][1000 genomes]
rs3744133	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3744136	0.88[AMR][1000 genomes]
rs3744140	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3826305	0.86[AMR][1000 genomes]
rs4073940	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4074611	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4074612	0.93[AMR][1000 genomes]
rs4074819	0.88[AMR][1000 genomes]
rs4264448	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4275916	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4283273	0.88[AMR][1000 genomes]
rs4321246	0.84[AMR][1000 genomes]
rs4606773	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4621033	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4985695	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4985697	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4985698	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4985703	0.88[AMR][1000 genomes]
rs4985712	1.00[ASN][1000 genomes]
rs4985714	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985715	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4985719	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4985723	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4985727	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4985739	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4985744	0.92[AMR][1000 genomes]
rs4985747	0.88[AMR][1000 genomes]
rs55751545	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56009207	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57812549	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58326998	0.88[AMR][1000 genomes]
rs58472573	0.97[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58814183	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59394251	0.88[AMR][1000 genomes]
rs60128647	0.93[AMR][1000 genomes]
rs61018209	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs7207187	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7210339	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7217970	0.92[AMR][1000 genomes]
rs7223583	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7223686	0.90[ASN][1000 genomes]
rs7223924	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73979053	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73979054	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73979055	0.80[AFR][1000 genomes]
rs73979058	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73979060	0.93[AMR][1000 genomes]
rs73979061	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73979081	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73979082	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73979083	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8064991	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8066111	0.88[AMR][1000 genomes]
rs8067563	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8075751	1.00[ASN][1000 genomes]
rs9910011	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058863	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv543227	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv907727	chr17:16892265-16938582	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv543231	chr17:16926227-16950644	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv978376	chr17:16934418-16938973	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16932200-16939800	Enhancers	Muscle Satellite Cultured Cells	--
2	chr17:16932400-16940600	Enhancers	HSMM	muscle
3	chr17:16932800-16944200	Weak transcription	Fetal Brain Female	brain
4	chr17:16934200-16937800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr17:16934600-16944600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr17:16935200-16940800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr17:16935400-16941200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr17:16935600-16937800	Weak transcription	Fetal Kidney	kidney
9	chr17:16935600-16944400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr17:16935800-16945200	Weak transcription	Aorta	Aorta
11	chr17:16936000-16938800	Weak transcription	Left Ventricle	heart
12	chr17:16936000-16938800	Weak transcription	Psoas Muscle	Psoas
13	chr17:16936000-16938800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr17:16936000-16938800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr17:16936000-16939000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr17:16936000-16939000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr17:16936000-16939200	Weak transcription	Placenta	Placenta
18	chr17:16936000-16939800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr17:16936000-16939800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr17:16936000-16939800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr17:16936000-16939800	Weak transcription	Spleen	Spleen
22	chr17:16936000-16940000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr17:16936000-16940000	Weak transcription	Lung	lung
24	chr17:16936000-16940000	Weak transcription	Right Atrium	heart
25	chr17:16936000-16940000	Weak transcription	NHLF	lung
26	chr17:16936000-16940200	Weak transcription	Pancreas	Pancrea
27	chr17:16936000-16942000	Weak transcription	Fetal Intestine Large	intestine
28	chr17:16936000-16943200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr17:16936000-16943400	Weak transcription	Fetal Brain Male	brain
30	chr17:16936000-16944200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr17:16936000-16944400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr17:16936000-16944400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr17:16936000-16944400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr17:16936000-16944400	Weak transcription	Colonic Mucosa	Colon
35	chr17:16936000-16944400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr17:16936000-16944400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr17:16936000-16944400	Enhancers	A549	lung
38	chr17:16936000-16944400	Weak transcription	NHEK	skin
39	chr17:16936000-16944600	Weak transcription	Gastric	stomach
40	chr17:16936000-16944600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr17:16936000-16944800	Weak transcription	Brain Angular Gyrus	brain
42	chr17:16936000-16944800	Weak transcription	Esophagus	oesophagus
43	chr17:16936200-16938600	Weak transcription	HepG2	liver
44	chr17:16936200-16938800	Weak transcription	Fetal Muscle Leg	muscle
45	chr17:16936200-16939000	Weak transcription	Fetal Stomach	stomach
46	chr17:16936200-16939400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr17:16936200-16939800	Weak transcription	NHDF-Ad	bronchial
48	chr17:16936200-16940000	Weak transcription	Adipose Nuclei	Adipose
49	chr17:16936200-16940000	Weak transcription	Hela-S3	cervix
50	chr17:16936200-16940800	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links