Variant report

Variant	rs17476879
Chromosome Location	chr4:15562013-15562014
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs16892232	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16892260	0.81[CEU][hapmap]
rs17385861	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17385951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17405797	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs17476642	0.91[CEU][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2302465	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs2302469	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs3756245	0.84[CEU][hapmap]
rs3822258	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4279202	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55735476	0.82[EUR][1000 genomes]
rs55784324	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55803452	0.84[EUR][1000 genomes]
rs55963737	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56065468	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56093715	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56094420	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56149419	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56166932	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73224650	0.85[EUR][1000 genomes]
rs73237154	0.82[EUR][1000 genomes]
rs73237171	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237172	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237182	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73237198	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239165	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239167	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239174	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239175	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239182	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239189	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239191	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239193	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73241109	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73241111	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73241112	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73241117	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73241120	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73241180	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73241183	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73241185	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73241190	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73241191	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73241195	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73241197	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73241198	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73243105	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73243107	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73243112	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73243114	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73243118	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73243126	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73243128	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73243129	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73243131	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73243132	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73243135	0.85[EUR][1000 genomes];1.00[ASN][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	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
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15487400-15570400	Weak transcription	Psoas Muscle	Psoas
2	chr4:15502800-15577600	Weak transcription	Right Ventricle	heart
3	chr4:15509200-15564400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:15512000-15580000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:15513000-15562400	Weak transcription	Primary B cells from cord blood	blood
6	chr4:15517800-15593600	Weak transcription	HUVEC	blood vessel
7	chr4:15520000-15572400	Weak transcription	Small Intestine	intestine
8	chr4:15537200-15565000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr4:15537400-15621000	Weak transcription	Hela-S3	cervix
10	chr4:15539000-15570400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr4:15540200-15562600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr4:15540400-15563200	Weak transcription	Brain Substantia Nigra	brain
13	chr4:15540400-15565000	Weak transcription	NHDF-Ad	bronchial
14	chr4:15543800-15570600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr4:15544400-15562400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr4:15544600-15563600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:15544800-15571600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr4:15544800-15576200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr4:15545000-15575600	Weak transcription	Fetal Heart	heart
20	chr4:15546000-15589600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:15546200-15564400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:15546200-15569400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr4:15546400-15572600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr4:15546800-15569200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr4:15548800-15570800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:15549400-15565600	Weak transcription	Primary T cells from cord blood	blood
27	chr4:15549600-15564400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr4:15549600-15570800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:15550000-15617800	Weak transcription	Thymus	Thymus
30	chr4:15554000-15563600	Strong transcription	Stomach Smooth Muscle	stomach
31	chr4:15554000-15572800	Strong transcription	Fetal Brain Female	brain
32	chr4:15554600-15601400	Weak transcription	A549	lung
33	chr4:15555000-15562400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr4:15555000-15566800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr4:15555600-15563200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr4:15555800-15565000	Weak transcription	Placenta	Placenta
37	chr4:15555800-15569200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr4:15555800-15589400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr4:15556000-15569200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr4:15556000-15603200	Weak transcription	Fetal Thymus	thymus
41	chr4:15557000-15564600	Weak transcription	Gastric	stomach
42	chr4:15557200-15562600	Weak transcription	Left Ventricle	heart
43	chr4:15557400-15564400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr4:15557400-15566600	Weak transcription	Colonic Mucosa	Colon
45	chr4:15557400-15567600	Weak transcription	Fetal Brain Male	brain
46	chr4:15557600-15563200	Weak transcription	Brain Hippocampus Middle	brain
47	chr4:15558000-15564600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:15558200-15565000	Weak transcription	Fetal Kidney	kidney
49	chr4:15558400-15563800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr4:15558400-15574600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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