Variant report

Variant	rs6554894
Chromosome Location	chr5:15690813-15690814
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11133822	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11133823	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11748700	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11958262	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12655356	0.82[AMR][1000 genomes]
rs13170407	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16867540	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17602392	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17602470	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4133004	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4235556	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4273603	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4289558	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4320259	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4330464	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4374756	0.81[AMR][1000 genomes]
rs4391163	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4391164	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4395631	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4435862	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4505949	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4582274	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4590179	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4702099	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56130171	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6554893	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6554895	0.81[EUR][1000 genomes]
rs6554898	0.88[AMR][1000 genomes]
rs6865314	0.80[AMR][1000 genomes]
rs6875955	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6891925	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6898184	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7713553	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7713555	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7724782	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7733271	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs924455	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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
5	nsv830214	chr5:15589809-15791032	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv3507774	chr5:15593461-15822407	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3507776	chr5:15593461-15822407	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1028089	chr5:15636285-15883910	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv537676	chr5:15636285-15883910	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1024248	chr5:15638067-15863583	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv537677	chr5:15638067-15863583	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv880755	chr5:15670377-15938553	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
13	nsv597263	chr5:15672137-15720478	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv461983	chr5:15674635-15720106	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv597264	chr5:15674635-15720106	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	esv2757107	chr5:15678556-15810987	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	esv2759327	chr5:15678556-15810987	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv432718	chr5:15688927-15723346	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 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	chr5:15675200-15693000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:15684000-15695200	Weak transcription	HUVEC	blood vessel
3	chr5:15684600-15691200	Weak transcription	Fetal Stomach	stomach
4	chr5:15684600-15694000	Weak transcription	Fetal Kidney	kidney
5	chr5:15684800-15693000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:15686600-15694400	Weak transcription	Fetal Lung	lung
7	chr5:15687800-15691000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr5:15687800-15691200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:15687800-15691200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:15687800-15691200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:15687800-15691400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr5:15687800-15694200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr5:15687800-15694200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:15688000-15694200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr5:15688200-15691200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:15688400-15704200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr5:15689200-15693000	Weak transcription	Lung	lung
18	chr5:15689400-15691200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr5:15689600-15691000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr5:15690000-15692200	Enhancers	HSMMtube	muscle
21	chr5:15690200-15691000	Weak transcription	Adipose Nuclei	Adipose
22	chr5:15690200-15692600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:15690200-15692600	Enhancers	Colon Smooth Muscle	Colon
24	chr5:15690200-15695000	Enhancers	NHDF-Ad	bronchial
25	chr5:15690600-15691400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:15690600-15691400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:15690600-15692200	Enhancers	Brain Hippocampus Middle	brain
28	chr5:15690600-15692800	Enhancers	Fetal Heart	heart
29	chr5:15690800-15691000	Enhancers	NH-A	brain
30	chr5:15690800-15691000	Enhancers	NHLF	lung
31	chr5:15690800-15691400	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr5:15690800-15691400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:15690800-15691400	Enhancers	Aorta	Aorta
34	chr5:15690800-15691400	Enhancers	Right Ventricle	heart
35	chr5:15690800-15691600	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr5:15690800-15691600	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr5:15690800-15691800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:15690800-15691800	Enhancers	Brain Substantia Nigra	brain
39	chr5:15690800-15691800	Enhancers	HSMM	muscle
40	chr5:15690800-15692000	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr5:15690800-15692000	Enhancers	Right Atrium	heart
42	chr5:15690800-15692200	Enhancers	Brain Angular Gyrus	brain
43	chr5:15690800-15692200	Enhancers	Brain Cingulate Gyrus	brain
44	chr5:15690800-15692200	Enhancers	Left Ventricle	heart
45	chr5:15690800-15692400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:15690800-15693200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:15690800-15695800	Enhancers	Brain Anterior Caudate	brain
48	chr5:15690800-15696200	Enhancers	Ovary	ovary
49	chr5:15690800-15696400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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