Variant report

Variant	rs62021880
Chromosome Location	chr15:55877704-55877705
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:55875375..55879008-chr15:55880167..55883388,4	K562	blood:
2	chr15:55871829..55873801-chr15:55877052..55878758,2	K562	blood:
3	chr15:55876611..55879059-chr15:55880096..55882468,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171016	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1051506	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11630020	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11634048	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11634055	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11634657	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11634919	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11635072	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11635978	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11637574	0.84[AMR][1000 genomes]
rs11637694	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11638846	0.91[EUR][1000 genomes]
rs11639329	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11639446	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11854594	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11858599	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11858624	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1926	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2414420	0.86[AFR][1000 genomes]
rs28456137	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28618157	1.00[EUR][1000 genomes]
rs28651966	0.98[EUR][1000 genomes]
rs34694682	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62020018	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs62020019	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs62020020	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs62020021	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62020022	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs62020023	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs62020033	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62020034	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs62020035	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs62020037	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs62020038	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62020039	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62020041	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62020043	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62020044	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62020045	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs62020047	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62020057	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62020058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62021860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62021861	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62021862	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62021863	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62021865	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62021866	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62021867	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs62021868	0.88[AFR][1000 genomes]
rs62021869	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62021870	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62021872	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs62021873	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62021874	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62021876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62021877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62021878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62021879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7181070	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7182121	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv531054	chr15:55571230-55914205	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv1041635	chr15:55658171-55943942	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription 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 target site	22 gene(s)	inside rSNPs	diseases
8	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv833016	chr15:55749169-55897906	Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1049774	chr15:55759573-56044600	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv569540	chr15:55866065-55950082	Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55846200-55878800	Weak transcription	HSMM	muscle
2	chr15:55858000-55879400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:55859600-55878800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr15:55861200-55878400	Weak transcription	Fetal Muscle Leg	muscle
5	chr15:55863800-55878200	Weak transcription	Fetal Brain Male	brain
6	chr15:55864000-55878200	Weak transcription	Fetal Lung	lung
7	chr15:55865600-55879000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:55866600-55878200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:55866600-55878800	Weak transcription	HSMMtube	muscle
10	chr15:55866600-55878800	Weak transcription	NHDF-Ad	bronchial
11	chr15:55866800-55878600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr15:55869400-55878800	Weak transcription	A549	lung
13	chr15:55870200-55878400	Weak transcription	Psoas Muscle	Psoas
14	chr15:55873000-55878800	Weak transcription	Ovary	ovary
15	chr15:55873200-55878000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:55874600-55878400	Weak transcription	Fetal Kidney	kidney
17	chr15:55875200-55877800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:55876200-55878600	Weak transcription	NH-A	brain
19	chr15:55876600-55879400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr15:55876800-55877800	Enhancers	Brain Germinal Matrix	brain
21	chr15:55877000-55877800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:55877200-55878200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr15:55877200-55878800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr15:55877400-55881600	Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr15:55877600-55878200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:55877600-55879000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:55877600-55879200	Active TSS	Fetal Brain Female	brain

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