Variant report

Variant	rs4558091
Chromosome Location	chr10:50321918-50321919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10218995	0.83[JPT][hapmap]
rs11100988	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11100989	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11100990	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12240534	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12246766	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12255055	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]
rs12267388	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12269023	0.83[MEX][hapmap];0.83[TSI][hapmap]
rs12765281	1.00[CHB][hapmap]
rs12776553	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13088	0.93[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17773851	1.00[CHB][hapmap]
rs17782733	1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[ASN][1000 genomes]
rs1986725	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs2002728	0.83[JPT][hapmap]
rs2003044	0.89[CHB][hapmap]
rs2377983	0.88[YRI][hapmap]
rs2466748	0.83[JPT][hapmap]
rs2466756	0.83[JPT][hapmap]
rs2725179	0.94[CHB][hapmap]
rs2725180	0.83[JPT][hapmap]
rs2725181	0.94[CHB][hapmap]
rs2725192	0.83[JPT][hapmap]
rs2725200	1.00[JPT][hapmap]
rs2804931	0.89[CHB][hapmap]
rs2804932	0.89[CHB][hapmap]
rs2804933	0.87[JPT][hapmap]
rs2804934	0.94[CHB][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs2804936	0.83[JPT][hapmap]
rs2804937	1.00[CHB][hapmap]
rs2804939	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs2804940	0.91[EUR][1000 genomes]
rs35007047	0.81[ASN][1000 genomes]
rs35285557	0.84[ASN][1000 genomes]
rs35666409	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36015645	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073711	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4073712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4240499	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4240500	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4319434	0.83[JPT][hapmap];0.80[MEX][hapmap]
rs4319435	0.82[JPT][hapmap]
rs4344406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4350286	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4364979	0.84[ASN][1000 genomes]
rs4403731	0.82[AMR][1000 genomes]
rs4412679	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4417190	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4497320	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4509682	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4532948	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4559606	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4620641	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4644582	0.84[ASN][1000 genomes]
rs4838365	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838367	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838446	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4838447	0.91[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6537497	0.96[CEU][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs6537499	0.83[JPT][hapmap];0.80[MEX][hapmap]
rs7072243	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7073645	0.83[JPT][hapmap]
rs7094217	0.83[JPT][hapmap];0.83[MEX][hapmap]
rs7097933	0.86[ASW][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs7100655	1.00[CHB][hapmap];0.81[CHD][hapmap]

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	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
6	nsv550817	chr10:50319387-50328494	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4558091	WDFY4	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50312600-50322800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:50315000-50322600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr10:50315400-50323000	Weak transcription	Pancreas	Pancrea
4	chr10:50315600-50323000	Weak transcription	Spleen	Spleen
5	chr10:50315800-50322200	Enhancers	Left Ventricle	heart
6	chr10:50315800-50322600	Weak transcription	Liver	Liver
7	chr10:50317400-50322000	Weak transcription	K562	blood
8	chr10:50318000-50322200	Weak transcription	Brain Anterior Caudate	brain
9	chr10:50318200-50322800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:50318600-50322200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr10:50319000-50322000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr10:50319000-50322800	Weak transcription	Esophagus	oesophagus
13	chr10:50319600-50322000	Weak transcription	Brain Hippocampus Middle	brain
14	chr10:50319600-50322600	Weak transcription	Psoas Muscle	Psoas
15	chr10:50319800-50323000	Weak transcription	Lung	lung
16	chr10:50320200-50322000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr10:50320400-50322200	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr10:50320400-50322400	Weak transcription	Colonic Mucosa	Colon
19	chr10:50320800-50322000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr10:50320800-50322000	Enhancers	Colon Smooth Muscle	Colon
21	chr10:50320800-50322200	Enhancers	Fetal Thymus	thymus
22	chr10:50320800-50322600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr10:50321000-50322000	Enhancers	Fetal Lung	lung
24	chr10:50321000-50322000	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
25	chr10:50321000-50322000	Enhancers	NHDF-Ad	bronchial
26	chr10:50321000-50322200	Enhancers	Right Atrium	heart
27	chr10:50321000-50323200	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr10:50321200-50322200	Weak transcription	Right Ventricle	heart
29	chr10:50321400-50322000	Enhancers	HSMM	muscle
30	chr10:50321400-50322200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr10:50321400-50322200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr10:50321400-50322400	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
33	chr10:50321600-50322000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr10:50321600-50322000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr10:50321600-50322400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr10:50321600-50322400	Flanking Active TSS	Ovary	ovary
37	chr10:50321600-50322400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr10:50321600-50322600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr10:50321600-50322600	Enhancers	Brain Angular Gyrus	brain
40	chr10:50321600-50322600	Flanking Active TSS	Osteobl	bone
41	chr10:50321600-50322800	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr10:50321600-50323000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr10:50321800-50322000	Enhancers	Aorta	Aorta
44	chr10:50321800-50322000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
45	chr10:50321800-50322000	Enhancers	NH-A	brain
46	chr10:50321800-50322000	Enhancers	NHLF	lung
47	chr10:50321800-50322200	Enhancers	Brain Substantia Nigra	brain
48	chr10:50321800-50322200	Flanking Active TSS	Fetal Muscle Trunk	muscle
49	chr10:50321800-50322400	Enhancers	Fetal Heart	heart
50	chr10:50321800-50322400	Flanking Active TSS	HSMMtube	muscle

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