Variant report

Variant	rs13088
Chromosome Location	chr10:50315893-50315894
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:50314500..50318570-chr10:50326499..50328270,3	K562	blood:
2	chr10:50303445..50305723-chr10:50315132..50317304,2	K562	blood:
3	chr10:50314896..50317280-chr10:50385638..50388577,2	K562	blood:

Variant related genes	Relation type
ENSG00000204161	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11100988	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11100989	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11100990	0.88[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12240534	0.81[CEU][hapmap];0.83[AMR][1000 genomes]
rs12245255	1.00[CHB][hapmap];0.84[CHD][hapmap];0.89[ASN][1000 genomes]
rs12246766	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12255055	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]
rs12267388	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12269023	0.83[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs12776553	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12777282	0.82[CHB][hapmap]
rs1986725	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs2377983	0.88[YRI][hapmap]
rs2804934	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs2804939	0.88[CEU][hapmap];0.91[GIH][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs2804940	0.88[EUR][1000 genomes]
rs35666409	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36015645	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4073711	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4073712	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4240499	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4240500	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4265516	1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs4298825	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs4317903	0.80[AMR][1000 genomes]
rs4319434	0.80[MEX][hapmap]
rs4344406	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4350286	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4403731	0.83[AMR][1000 genomes]
rs4412679	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4417190	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4421675	1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs4488117	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs4497320	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4509682	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4532948	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4558089	1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs4558091	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]
rs4559606	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4620641	0.92[CEU][hapmap];0.98[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4838365	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4838367	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4838446	0.93[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.97[LWK][hapmap];0.95[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]
rs4838447	0.91[CEU][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6537497	0.96[CEU][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs6537499	0.80[MEX][hapmap]
rs7069758	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs7072243	0.81[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7079570	0.92[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs7094217	0.83[MEX][hapmap]
rs7097933	0.87[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13088	WDFY4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50304800-50317600	Weak transcription	Fetal Heart	heart
2	chr10:50311800-50317800	Weak transcription	Fetal Intestine Large	intestine
3	chr10:50312200-50320400	Enhancers	Colon Smooth Muscle	Colon
4	chr10:50312400-50316200	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr10:50312600-50316400	Weak transcription	K562	blood
6	chr10:50312600-50317000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr10:50312600-50322800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:50314400-50316000	Enhancers	Brain Angular Gyrus	brain
9	chr10:50314400-50316200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr10:50314400-50316200	Enhancers	Brain Anterior Caudate	brain
11	chr10:50314400-50321400	Genic enhancers	Fetal Stomach	stomach
12	chr10:50314600-50316000	Genic enhancers	Right Ventricle	heart
13	chr10:50314600-50316600	Enhancers	Fetal Thymus	thymus
14	chr10:50314600-50318000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr10:50314600-50318000	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr10:50314600-50318000	Enhancers	Placenta	Placenta
17	chr10:50314600-50319800	Enhancers	Lung	lung
18	chr10:50314600-50320200	Enhancers	Right Atrium	heart
19	chr10:50314600-50321000	Genic enhancers	Fetal Muscle Leg	muscle
20	chr10:50314800-50316200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr10:50315000-50317800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr10:50315000-50318800	Weak transcription	Psoas Muscle	Psoas
23	chr10:50315000-50322600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr10:50315200-50316000	Genic enhancers	Ovary	ovary
25	chr10:50315200-50316200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr10:50315200-50318000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr10:50315400-50317000	Strong transcription	Fetal Intestine Small	intestine
28	chr10:50315400-50317800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr10:50315400-50319400	Weak transcription	Aorta	Aorta
30	chr10:50315400-50319600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr10:50315400-50323000	Weak transcription	Pancreas	Pancrea
32	chr10:50315600-50316000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr10:50315600-50316000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr10:50315600-50317000	Weak transcription	Colonic Mucosa	Colon
35	chr10:50315600-50317000	Weak transcription	NHDF-Ad	bronchial
36	chr10:50315600-50317200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr10:50315600-50317200	Weak transcription	NHLF	lung
38	chr10:50315600-50317600	Weak transcription	Brain Hippocampus Middle	brain
39	chr10:50315600-50317800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr10:50315600-50323000	Weak transcription	Spleen	Spleen
41	chr10:50315800-50316800	Weak transcription	HSMMtube	muscle
42	chr10:50315800-50317000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr10:50315800-50317200	Weak transcription	Adipose Nuclei	Adipose
44	chr10:50315800-50317200	Weak transcription	Brain Substantia Nigra	brain
45	chr10:50315800-50317200	Enhancers	Stomach Smooth Muscle	stomach
46	chr10:50315800-50317800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr10:50315800-50317800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr10:50315800-50318000	Weak transcription	Esophagus	oesophagus
49	chr10:50315800-50320600	Enhancers	Fetal Lung	lung
50	chr10:50315800-50322200	Enhancers	Left Ventricle	heart

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