Variant report

Variant	rs9790561
Chromosome Location	chr4:53988175-53988176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:53987651..53991411-chr4:53993052..53996048,3	K562	blood:
2	chr4:53977404..53979718-chr4:53987877..53989562,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10013152	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs10024057	0.90[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs10033650	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10517278	0.85[GIH][hapmap]
rs11941906	0.90[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs13142315	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13340297	1.00[CEU][hapmap]
rs1384696	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs17082301	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs17082330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs2062185	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs2062186	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs28688668	0.94[EUR][1000 genomes]
rs28882784	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4864445	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4864712	0.90[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4864715	0.90[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4864717	0.83[GIH][hapmap]
rs56259272	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62338998	0.91[EUR][1000 genomes]
rs6554065	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6822707	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6855010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7658716	0.90[CHB][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap]
rs7671836	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7694940	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7698034	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53978800-54008000	Weak transcription	Primary T cells from cord blood	blood
2	chr4:53980400-53993000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr4:53982200-53989600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:53984800-53989600	Enhancers	Brain Substantia Nigra	brain
5	chr4:53985200-53988200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr4:53985600-53989600	Enhancers	Fetal Intestine Small	intestine
7	chr4:53985600-53990200	Enhancers	Stomach Mucosa	stomach
8	chr4:53985600-53991400	Enhancers	HepG2	liver
9	chr4:53985800-53988600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:53985800-53988800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:53985800-53988800	Enhancers	Right Atrium	heart
12	chr4:53985800-53989000	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr4:53985800-53989600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:53985800-53989600	Enhancers	Fetal Lung	lung
15	chr4:53986000-53989400	Enhancers	Brain Anterior Caudate	brain
16	chr4:53986200-53993000	Weak transcription	Fetal Stomach	stomach
17	chr4:53986200-53993200	Weak transcription	Fetal Kidney	kidney
18	chr4:53986200-53993600	Weak transcription	Psoas Muscle	Psoas
19	chr4:53986600-53988200	Weak transcription	Colonic Mucosa	Colon
20	chr4:53986600-53989800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr4:53986600-53993600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:53986600-53994600	Weak transcription	Colon Smooth Muscle	Colon
23	chr4:53986800-53988400	Weak transcription	Fetal Intestine Large	intestine
24	chr4:53986800-53989600	Weak transcription	Placenta	Placenta
25	chr4:53986800-53990000	Enhancers	Brain Hippocampus Middle	brain
26	chr4:53986800-53990400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr4:53986800-54010800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:53986800-54011000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr4:53987200-53988400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:53987200-53988600	Enhancers	Brain Cingulate Gyrus	brain
31	chr4:53987200-53989000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:53987400-53989000	Enhancers	Brain Angular Gyrus	brain
33	chr4:53987400-53989800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:53987400-53990200	Enhancers	Small Intestine	intestine
35	chr4:53987600-53991200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr4:53987600-53993600	Weak transcription	Fetal Muscle Leg	muscle
37	chr4:53987800-53993600	Weak transcription	Aorta	Aorta
38	chr4:53987800-53993800	Weak transcription	Adipose Nuclei	Adipose
39	chr4:53987800-54016800	Weak transcription	NHLF	lung
40	chr4:53988000-53990400	Enhancers	Liver	Liver
41	chr4:53988000-53992800	Weak transcription	Ovary	ovary
42	chr4:53988000-53993800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:53988000-53994400	Weak transcription	NHDF-Ad	bronchial
44	chr4:53988000-53997600	Weak transcription	Osteobl	bone

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