Variant report

Variant	rs10005413
Chromosome Location	chr4:148904042-148904043
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10021991	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395296	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17024193	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17024220	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs17024245	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17476251	0.81[EUR][1000 genomes]
rs17476412	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17579683	0.81[EUR][1000 genomes]
rs2575582	1.00[CEU][hapmap]
rs28410093	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28607979	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60201372	0.81[EUR][1000 genomes]
rs61080266	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6849257	0.81[AFR][1000 genomes]
rs7657316	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv880244	chr4:148764252-148920089	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1029845	chr4:148766290-148916437	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1030001	chr4:148773479-148916437	Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1017904	chr4:148814133-148975348	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148866400-148927400	Weak transcription	Thymus	Thymus
2	chr4:148885600-148905200	Weak transcription	Fetal Intestine Small	intestine
3	chr4:148885600-148905400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:148885600-148939000	Weak transcription	Pancreas	Pancrea
5	chr4:148885800-148907000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:148885800-148912800	Weak transcription	Fetal Lung	lung
7	chr4:148886000-148917600	Weak transcription	Esophagus	oesophagus
8	chr4:148889000-148905400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:148889200-148936200	Weak transcription	Fetal Intestine Large	intestine
10	chr4:148889400-148905400	Weak transcription	NHLF	lung
11	chr4:148891400-148905000	Weak transcription	Stomach Mucosa	stomach
12	chr4:148891400-148905400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:148891600-148905400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:148891600-148912800	Weak transcription	Fetal Kidney	kidney
15	chr4:148891600-148920600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:148891600-148928000	Weak transcription	A549	lung
17	chr4:148896600-148928400	Weak transcription	Spleen	Spleen
18	chr4:148897200-148905200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:148897200-148905400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:148897200-148905400	Weak transcription	Aorta	Aorta
21	chr4:148897200-148905400	Weak transcription	Left Ventricle	heart
22	chr4:148897200-148905400	Weak transcription	Right Atrium	heart
23	chr4:148897200-148905600	Weak transcription	Gastric	stomach
24	chr4:148897200-148917600	Weak transcription	Lung	lung
25	chr4:148897600-148904800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr4:148898000-148905000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:148898000-148905000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr4:148898200-148905200	Weak transcription	Fetal Stomach	stomach
29	chr4:148898200-148920600	Weak transcription	NHEK	skin
30	chr4:148898200-148925400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:148899000-148905400	Weak transcription	Ovary	ovary
32	chr4:148899600-148905000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:148899800-148904800	Weak transcription	Fetal Muscle Leg	muscle
34	chr4:148900800-148911400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:148902000-148905200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr4:148902000-148908400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr4:148902200-148905000	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:148902400-148905200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr4:148902600-148905200	Weak transcription	Adipose Nuclei	Adipose
40	chr4:148903000-148911200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:148903200-148905200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:148903200-148905400	Weak transcription	Fetal Heart	heart
43	chr4:148903200-148914800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:148903400-148904800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:148903400-148905000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:148903400-148907600	Weak transcription	HSMM	muscle
47	chr4:148903400-148914600	Weak transcription	HSMMtube	muscle
48	chr4:148903400-148914800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr4:148903400-148915000	Weak transcription	Osteobl	bone
50	chr4:148903800-148906000	ZNF genes & repeats	GM12878-XiMat	blood

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