Variant report

Variant	rs17004581
Chromosome Location	chr21:44996574-44996575
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:44992733..44995212-chr21:44995916..44999586,3	MCF-7	breast:
2	chr21:44846010..44848795-chr21:44996271..44998829,2	MCF-7	breast:
3	chr21:44995436..44998178-chr21:44998491..45000722,2	K562	blood:
4	chr21:44935745..44939889-chr21:44996444..44998643,4	MCF-7	breast:
5	chr21:44987600..44989351-chr21:44995707..44998533,2	K562	blood:

Variant related genes	Relation type
ENSG00000142178	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10427514	0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs10483077	0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10483078	0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs11089065	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11089090	0.90[YRI][hapmap]
rs11908893	0.81[AFR][1000 genomes]
rs11908919	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11909195	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11909530	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11909813	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11909916	0.83[AMR][1000 genomes]
rs11909999	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11910220	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11910351	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11910352	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11911293	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs11911483	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11911560	0.84[AFR][1000 genomes]
rs11911735	0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11911856	0.90[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12106371	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12106423	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12106466	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs13339951	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17004507	0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004580	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17004582	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17004585	0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004586	0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004587	0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004588	0.81[AFR][1000 genomes]
rs17004589	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004590	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17004592	0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004593	0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004594	0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004595	0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs17004596	0.90[YRI][hapmap];0.83[AMR][1000 genomes]
rs2117981	0.82[AFR][1000 genomes]
rs28431406	0.83[AMR][1000 genomes]
rs28782771	0.83[AMR][1000 genomes]
rs28852206	0.83[AMR][1000 genomes]
rs59298188	0.85[AMR][1000 genomes]
rs7283618	0.84[AFR][1000 genomes]
rs7510543	0.83[AFR][1000 genomes]
rs9917493	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv913873	chr21:44879869-45142427	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv1061539	chr21:44915533-45041824	Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1067171	chr21:44921187-45039471	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv521700	chr21:44925334-45041790	Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
5	nsv470903	chr21:44925334-45061501	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
6	nsv459289	chr21:44925334-45064600	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
7	nsv587690	chr21:44925334-45064600	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
8	nsv1065359	chr21:44967209-45029878	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
9	nsv3537	chr21:44967340-45013104	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv834106	chr21:44992387-45109489	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44980400-44998400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr21:44987200-45005000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr21:44987200-45005000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr21:44988800-44996600	Enhancers	HSMMtube	muscle
5	chr21:44989000-44998000	Weak transcription	Gastric	stomach
6	chr21:44992400-45004200	Weak transcription	Right Atrium	heart
7	chr21:44995000-45002000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr21:44995000-45005400	Weak transcription	Ovary	ovary
9	chr21:44995000-45024200	Weak transcription	Fetal Brain Male	brain
10	chr21:44995200-45001600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr21:44995200-45001600	Weak transcription	Lung	lung
12	chr21:44995200-45006000	Weak transcription	Spleen	Spleen
13	chr21:44995400-44998600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr21:44995400-45001600	Weak transcription	Placenta	Placenta
15	chr21:44995600-44998200	Weak transcription	Fetal Lung	lung
16	chr21:44995600-44998400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr21:44995600-44998600	Weak transcription	HSMM	muscle
18	chr21:44995800-44998200	Weak transcription	Fetal Stomach	stomach
19	chr21:44995800-44998400	Weak transcription	Fetal Muscle Leg	muscle
20	chr21:44996000-44998400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr21:44996200-45005800	Weak transcription	Rectal Smooth Muscle	rectum

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