Variant report

Variant	rs10022530
Chromosome Location	chr4:15475100-15475101
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10000250	0.93[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10012928	1.00[ASN][1000 genomes]
rs10033082	0.81[AMR][1000 genomes]
rs10212846	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1024757	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs1024760	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4423869	1.00[CEU][hapmap]
rs4698110	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4698382	0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838330	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs719993	0.87[CEU][hapmap]
rs7665294	0.81[AMR][1000 genomes]
rs9990934	0.87[CEU][hapmap]
rs9993580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9993656	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9994702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995927	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10022530	FBXL5	cis	multi-tissue	Pritchard
rs10022530	FAM200B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15471800-15480800	Weak transcription	Pancreas	Pancrea
2	chr4:15471800-15481000	Weak transcription	Spleen	Spleen
3	chr4:15472200-15475600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr4:15472200-15475600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr4:15472200-15477800	Weak transcription	Left Ventricle	heart
6	chr4:15472200-15480600	Weak transcription	HSMM	muscle
7	chr4:15472200-15480800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:15472200-15480800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:15472200-15480800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:15472200-15480800	Weak transcription	Fetal Intestine Large	intestine
11	chr4:15472200-15480800	Weak transcription	Fetal Intestine Small	intestine
12	chr4:15472200-15480800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr4:15472200-15480800	Weak transcription	Lung	lung
14	chr4:15472600-15477800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:15472600-15480800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:15472800-15480800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:15472800-15480800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr4:15472800-15480800	Weak transcription	NHLF	lung
19	chr4:15473000-15475200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr4:15473000-15477200	Weak transcription	Ovary	ovary
21	chr4:15473000-15477800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:15473000-15480400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr4:15473000-15480800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:15473000-15480800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr4:15473000-15480800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:15473000-15480800	Weak transcription	Fetal Kidney	kidney
27	chr4:15473000-15480800	Weak transcription	Psoas Muscle	Psoas
28	chr4:15473200-15477200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr4:15473200-15477400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:15473200-15477600	Weak transcription	Fetal Muscle Leg	muscle
31	chr4:15473200-15477800	Weak transcription	Adipose Nuclei	Adipose
32	chr4:15473200-15477800	Weak transcription	Aorta	Aorta
33	chr4:15473200-15480800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:15473200-15480800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr4:15473200-15480800	Weak transcription	Fetal Heart	heart
36	chr4:15473200-15480800	Weak transcription	Fetal Lung	lung
37	chr4:15473200-15480800	Weak transcription	Fetal Stomach	stomach
38	chr4:15473200-15480800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr4:15473800-15475800	Enhancers	Colon Smooth Muscle	Colon
40	chr4:15473800-15476000	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr4:15474000-15480800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr4:15474400-15475400	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr4:15474400-15475800	Enhancers	Stomach Smooth Muscle	stomach
44	chr4:15474400-15476000	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr4:15474400-15476000	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr4:15474600-15475200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:15474600-15475400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr4:15474800-15475200	Weak transcription	HSMMtube	muscle
49	chr4:15474800-15475400	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr4:15475000-15475800	Enhancers	H9 Cell Line	embryonic stem cell

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