Variant report

Variant	rs6554887
Chromosome Location	chr5:15576130-15576131
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10037317	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13184823	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1366651	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1366653	0.93[CEU][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1429037	0.94[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1429039	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1429040	0.93[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1429041	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1835130	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1835131	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1835132	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1835133	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1978633	0.89[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2402166	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2402167	0.93[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4702084	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4702086	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6420022	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6420023	0.85[ASN][1000 genomes]
rs6554888	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6895002	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7733607	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7734082	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9312893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9312894	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs969351	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs972182	0.93[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs983889	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[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	nsv516929	chr5:15087791-15870300	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1023068	chr5:15095221-15863583	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv869040	chr5:15097602-15866117	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv530222	chr5:15151662-15851485	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15555800-15584200	Weak transcription	HSMM	muscle
2	chr5:15567200-15580600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:15570600-15576200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:15571000-15577200	Weak transcription	Right Ventricle	heart
5	chr5:15571400-15581000	Enhancers	Fetal Heart	heart
6	chr5:15571800-15578200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:15572000-15578000	Weak transcription	Psoas Muscle	Psoas
8	chr5:15572000-15583600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:15572000-15583800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:15572800-15583200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:15573000-15576600	Enhancers	Colon Smooth Muscle	Colon
12	chr5:15573000-15583800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:15573200-15583600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr5:15573400-15577200	Weak transcription	Left Ventricle	heart
15	chr5:15573600-15579600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:15573800-15576200	Enhancers	Rectal Smooth Muscle	rectum
17	chr5:15574000-15577000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:15574000-15594200	Weak transcription	Fetal Kidney	kidney
19	chr5:15574400-15576400	Weak transcription	HUVEC	blood vessel
20	chr5:15574800-15576200	Enhancers	Fetal Stomach	stomach
21	chr5:15575000-15576200	Flanking Active TSS	Fetal Lung	lung
22	chr5:15575000-15576600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr5:15575200-15576400	Weak transcription	Fetal Muscle Leg	muscle
24	chr5:15575200-15576400	Weak transcription	Ovary	ovary
25	chr5:15575200-15579200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:15575400-15576800	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr5:15575400-15577200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:15575600-15576600	Enhancers	Brain Cingulate Gyrus	brain
29	chr5:15575600-15576800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr5:15575600-15577400	Weak transcription	Aorta	Aorta
31	chr5:15575600-15583600	Weak transcription	HSMMtube	muscle
32	chr5:15575800-15576200	Enhancers	Brain Substantia Nigra	brain
33	chr5:15575800-15577200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr5:15575800-15577200	Weak transcription	Osteobl	bone
35	chr5:15575800-15578000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:15575800-15578200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr5:15575800-15582800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr5:15576000-15576200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr5:15576000-15576200	Enhancers	Stomach Smooth Muscle	stomach
40	chr5:15576000-15576600	Enhancers	Brain Hippocampus Middle	brain
41	chr5:15576000-15576800	Weak transcription	Brain Angular Gyrus	brain
42	chr5:15576000-15577600	Enhancers	Brain Anterior Caudate	brain
43	chr5:15576000-15578000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr5:15576000-15578000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr5:15576000-15578800	Weak transcription	Fetal Brain Male	brain
46	chr5:15576000-15582600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:15576000-15584200	Weak transcription	Adipose Nuclei	Adipose
48	chr5:15576000-15584800	Weak transcription	NHLF	lung
49	chr5:15576000-15585200	Weak transcription	NHDF-Ad	bronchial

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