Variant report

Variant	rs10024057
Chromosome Location	chr4:53888072-53888073
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10013152	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs11941906	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13340297	0.87[CEU][hapmap]
rs1384696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17082301	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs17082330	0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[ASN][1000 genomes]
rs2062185	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2062186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28404612	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28507473	0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28592856	1.00[ASN][1000 genomes]
rs28652757	0.93[ASN][1000 genomes]
rs28688668	0.97[ASN][1000 genomes]
rs28713187	1.00[ASN][1000 genomes]
rs3912335	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4419529	1.00[ASN][1000 genomes]
rs4864712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4864713	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4864714	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4864715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6554065	0.90[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs6822707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6825075	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6855010	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7658716	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.97[ASN][1000 genomes]
rs7671836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7673017	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7694940	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7698034	0.97[ASN][1000 genomes]
rs9312635	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9790561	0.90[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs9999433	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	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv508280	chr4:53825060-53907661	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53879400-53888400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr4:53879400-53889600	Weak transcription	Aorta	Aorta
3	chr4:53879800-53888600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:53879800-53890000	Weak transcription	GM12878-XiMat	blood
5	chr4:53880400-53891800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:53880800-53892800	Weak transcription	Primary T cells from cord blood	blood
7	chr4:53882600-53888200	Weak transcription	Fetal Stomach	stomach
8	chr4:53883200-53896400	Weak transcription	Primary B cells from cord blood	blood
9	chr4:53884400-53889600	Enhancers	Ovary	ovary
10	chr4:53885600-53888800	Enhancers	NHDF-Ad	bronchial
11	chr4:53886000-53888800	Enhancers	NHLF	lung
12	chr4:53886200-53891200	Enhancers	Psoas Muscle	Psoas
13	chr4:53886200-53892400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr4:53886400-53889200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:53886400-53892400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:53886600-53889400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:53886800-53890000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:53886800-53890200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:53887000-53888200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:53887000-53888800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:53887000-53889000	Weak transcription	Pancreas	Pancrea
22	chr4:53887000-53892400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:53887200-53892400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr4:53887400-53888400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:53887400-53888600	Weak transcription	Osteobl	bone
26	chr4:53887600-53889400	Enhancers	Colon Smooth Muscle	Colon
27	chr4:53887800-53888800	Enhancers	Fetal Kidney	kidney
28	chr4:53887800-53889200	Enhancers	HSMMtube	muscle
29	chr4:53887800-53889600	Enhancers	Fetal Heart	heart
30	chr4:53888000-53888200	Enhancers	Left Ventricle	heart
31	chr4:53888000-53888200	Enhancers	Rectal Smooth Muscle	rectum
32	chr4:53888000-53888200	Enhancers	Right Atrium	heart
33	chr4:53888000-53888400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:53888000-53888600	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr4:53888000-53888600	Active TSS	Small Intestine	intestine
36	chr4:53888000-53888800	Enhancers	Fetal Brain Female	brain
37	chr4:53888000-53888800	Enhancers	Fetal Muscle Leg	muscle
38	chr4:53888000-53889400	Enhancers	Adipose Nuclei	Adipose
39	chr4:53888000-53889400	Enhancers	Fetal Lung	lung
40	chr4:53888000-53889400	Enhancers	Stomach Smooth Muscle	stomach
41	chr4:53888000-53890000	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr4:53888000-53890600	Enhancers	Skeletal Muscle Female	skeletal muscle

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