Variant report

Variant	rs4928058
Chromosome Location	chr3:100610854-100610855
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100538000..100539397-chr3:100609627..100610909,8	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1370160	1.00[ASW][hapmap];0.82[CHD][hapmap];0.84[LWK][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs1370161	0.82[AFR][1000 genomes]
rs1436941	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs1836986	1.00[ASW][hapmap];0.82[CHD][hapmap];0.95[LWK][hapmap];0.82[MKK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1836988	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs1987384	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.98[LWK][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2083008	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2083009	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2118172	0.83[ASW][hapmap];0.86[CHD][hapmap];0.86[MEX][hapmap]
rs2317331	0.83[YRI][hapmap]
rs3821725	0.94[ASW][hapmap];0.98[LWK][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4928093	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs4928094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786325	0.94[ASW][hapmap];0.95[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs6786332	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs975536	0.86[CHD][hapmap];0.80[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv514163	chr3:100547342-100670846	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4928058	SENP7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100594400-100618200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:100594600-100616800	Weak transcription	Ovary	ovary
3	chr3:100598600-100612400	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:100599600-100645400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:100599800-100618200	Weak transcription	Fetal Lung	lung
6	chr3:100602200-100616800	Weak transcription	NHDF-Ad	bronchial
7	chr3:100604200-100612200	Weak transcription	Psoas Muscle	Psoas
8	chr3:100604200-100617000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:100604400-100611200	Weak transcription	HSMMtube	muscle
10	chr3:100606600-100612000	Enhancers	Hela-S3	cervix
11	chr3:100610200-100611000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr3:100610200-100611000	Enhancers	Osteobl	bone
13	chr3:100610200-100612200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:100610400-100612000	Strong transcription	Stomach Smooth Muscle	stomach
15	chr3:100610400-100613400	Strong transcription	Fetal Muscle Leg	muscle
16	chr3:100610400-100617600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:100610600-100611000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:100610600-100612200	Strong transcription	Fetal Stomach	stomach
19	chr3:100610600-100617000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:100610600-100619200	Weak transcription	Fetal Intestine Large	intestine
21	chr3:100610800-100617000	Weak transcription	HSMM	muscle

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