Variant report

Variant	rs6554998
Chromosome Location	chr5:17360454-17360455
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:17216728..17218408-chr5:17358754..17361119,2	MCF-7	breast:
2	chr5:17306150..17307962-chr5:17359469..17361900,2	MCF-7	breast:
3	chr5:17336392..17339049-chr5:17358419..17360973,2	MCF-7	breast:
4	chr5:17358851..17361817-chr5:17363155..17365630,2	K562	blood:

Variant related genes	Relation type
ENSG00000185296	Chromatin interaction
ENSG00000215196	Chromatin interaction
ENSG00000176788	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs13178605	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1500506	0.90[ASN][1000 genomes]
rs1500507	0.90[ASN][1000 genomes]
rs1972037	0.91[ASN][1000 genomes]
rs2055875	0.87[ASN][1000 genomes]
rs298552	0.86[EUR][1000 genomes]
rs298553	0.86[EUR][1000 genomes]
rs34875290	0.90[ASN][1000 genomes]
rs35497365	0.91[ASN][1000 genomes]
rs4382171	0.90[ASN][1000 genomes]
rs4701683	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4701684	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4701685	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4702207	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4702208	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58439032	0.80[ASN][1000 genomes]
rs6554994	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554995	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554996	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6554997	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6861179	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6876143	0.91[ASN][1000 genomes]
rs6887129	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6892106	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7705848	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7706156	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7715898	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7727410	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7730990	0.88[ASN][1000 genomes]
rs7733712	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs867356	0.90[ASN][1000 genomes]
rs964751	0.89[ASN][1000 genomes]
rs964752	0.89[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	nsv1029959	chr5:17133214-17455995	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv461988	chr5:17296342-17484038	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv597313	chr5:17296342-17484038	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv830219	chr5:17325802-17518914	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 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	chr5:17354800-17366000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:17359000-17360800	Enhancers	NHDF-Ad	bronchial
3	chr5:17359400-17360800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:17359600-17361800	Enhancers	Placenta Amnion	Placenta Amnion
5	chr5:17359800-17360600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:17359800-17362600	Enhancers	Placenta	Placenta
7	chr5:17360000-17360600	Enhancers	Fetal Muscle Leg	muscle
8	chr5:17360000-17360800	Enhancers	NHLF	lung
9	chr5:17360000-17361600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:17360200-17360600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:17360200-17360600	Enhancers	Muscle Satellite Cultured Cells	--
12	chr5:17360200-17360800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:17360200-17360800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:17360200-17361600	Weak transcription	HMEC	breast
15	chr5:17360400-17360600	Flanking Active TSS	HSMM	muscle
16	chr5:17360400-17360600	Enhancers	HSMMtube	muscle
17	chr5:17360400-17360800	Enhancers	Fetal Muscle Trunk	muscle
18	chr5:17360400-17360800	Enhancers	Osteobl	bone
19	chr5:17360400-17361000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:17360400-17361000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:17360400-17361000	Enhancers	Fetal Stomach	stomach

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