Variant report

Variant	rs12255055
Chromosome Location	chr10:50318484-50318485
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:50314500..50318570-chr10:50326499..50328270,3	K562	blood:
2	chr10:50298074..50299624-chr10:50316267..50318551,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs11100988	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11100989	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11100990	0.82[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12198	0.83[JPT][hapmap]
rs12240534	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12246766	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12267388	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12269023	0.81[ASW][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs12765281	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12776553	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13088	0.81[ASW][hapmap];0.87[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17701186	0.86[ASN][1000 genomes]
rs17773851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17782733	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs1986725	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2003044	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2490838	0.85[ASN][1000 genomes]
rs2725179	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2725181	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2725184	0.84[ASN][1000 genomes]
rs2725185	0.85[ASN][1000 genomes]
rs2725190	0.85[ASN][1000 genomes]
rs2725200	0.81[CHB][hapmap]
rs2804930	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2804931	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2804932	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2804934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs2804935	0.83[JPT][hapmap]
rs2804937	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2804938	0.83[JPT][hapmap]
rs2804939	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2804940	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2804941	0.84[ASN][1000 genomes]
rs34056748	0.94[ASN][1000 genomes]
rs34062275	0.86[ASN][1000 genomes]
rs34110351	0.86[ASN][1000 genomes]
rs34436721	0.84[ASN][1000 genomes]
rs34467986	0.86[ASN][1000 genomes]
rs34589684	0.86[ASN][1000 genomes]
rs34786393	0.94[ASN][1000 genomes]
rs35007047	0.97[ASN][1000 genomes]
rs35285557	0.99[ASN][1000 genomes]
rs35666409	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36015645	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4073138	0.84[ASN][1000 genomes]
rs4073139	0.84[ASN][1000 genomes]
rs4073711	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4073712	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs4240499	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4240500	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4344406	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4350286	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4364979	0.99[ASN][1000 genomes]
rs4412679	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4417190	1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4495812	0.85[ASN][1000 genomes]
rs4497320	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4509682	0.86[ASW][hapmap];0.87[CEU][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4532948	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4558089	0.82[GIH][hapmap]
rs4558091	0.87[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4559606	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4620641	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4644582	0.99[ASN][1000 genomes]
rs4838365	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4838367	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4838446	0.87[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4838447	0.93[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55947405	0.84[ASN][1000 genomes]
rs58893558	0.94[ASN][1000 genomes]
rs6537497	0.83[CEU][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap]
rs67269950	0.84[ASN][1000 genomes]
rs7072243	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7081243	0.86[ASN][1000 genomes]
rs7100655	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[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	nsv831866	chr10:50165180-50335276	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	esv2761593	chr10:50276812-50336129	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	esv1824894	chr10:50309905-50340304	Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12255055	WDFY4	cis	parietal	SCAN
rs12255055	MAPK8	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50312200-50320400	Enhancers	Colon Smooth Muscle	Colon
2	chr10:50312600-50322800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:50314400-50321400	Genic enhancers	Fetal Stomach	stomach
4	chr10:50314600-50319800	Enhancers	Lung	lung
5	chr10:50314600-50320200	Enhancers	Right Atrium	heart
6	chr10:50314600-50321000	Genic enhancers	Fetal Muscle Leg	muscle
7	chr10:50315000-50318800	Weak transcription	Psoas Muscle	Psoas
8	chr10:50315000-50322600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr10:50315400-50319400	Weak transcription	Aorta	Aorta
10	chr10:50315400-50319600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr10:50315400-50323000	Weak transcription	Pancreas	Pancrea
12	chr10:50315600-50323000	Weak transcription	Spleen	Spleen
13	chr10:50315800-50320600	Enhancers	Fetal Lung	lung
14	chr10:50315800-50322200	Enhancers	Left Ventricle	heart
15	chr10:50315800-50322600	Weak transcription	Liver	Liver
16	chr10:50316000-50321200	Enhancers	Right Ventricle	heart
17	chr10:50316000-50321600	Enhancers	Ovary	ovary
18	chr10:50316600-50320200	Weak transcription	Fetal Thymus	thymus
19	chr10:50317000-50320400	Enhancers	NHDF-Ad	bronchial
20	chr10:50317200-50318800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr10:50317200-50319200	Enhancers	Brain Substantia Nigra	brain
22	chr10:50317200-50319400	Enhancers	Brain Angular Gyrus	brain
23	chr10:50317200-50320600	Enhancers	NHLF	lung
24	chr10:50317200-50321000	Enhancers	Adipose Nuclei	Adipose
25	chr10:50317200-50321600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr10:50317200-50321600	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr10:50317400-50319000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr10:50317400-50322000	Weak transcription	K562	blood
29	chr10:50317600-50318600	Enhancers	Fetal Heart	heart
30	chr10:50317600-50318600	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr10:50317800-50318600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr10:50317800-50318600	Enhancers	Brain Cingulate Gyrus	brain
33	chr10:50317800-50318600	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr10:50317800-50319000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr10:50317800-50319200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr10:50318000-50318600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr10:50318000-50318600	Enhancers	Fetal Muscle Trunk	muscle
38	chr10:50318000-50318800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr10:50318000-50319000	Weak transcription	Placenta	Placenta
40	chr10:50318000-50320600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr10:50318000-50321800	Enhancers	HSMMtube	muscle
42	chr10:50318000-50322200	Weak transcription	Brain Anterior Caudate	brain
43	chr10:50318200-50318600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
44	chr10:50318200-50318600	Enhancers	Osteobl	bone
45	chr10:50318200-50318800	Weak transcription	Esophagus	oesophagus
46	chr10:50318200-50319800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr10:50318200-50322800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr10:50318400-50318600	Enhancers	Duodenum Mucosa	Duodenum
49	chr10:50318400-50318600	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr10:50318400-50319000	Enhancers	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links