Variant report

Variant	rs59942474
Chromosome Location	chr3:178677375-178677376
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10804875	0.86[ASN][1000 genomes]
rs10936987	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10936988	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11715852	0.93[EUR][1000 genomes]
rs11716079	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11918186	0.93[EUR][1000 genomes]
rs11926798	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4245916	0.86[ASN][1000 genomes]
rs4254707	0.87[ASN][1000 genomes]
rs4328857	0.86[ASN][1000 genomes]
rs4583702	0.84[ASN][1000 genomes]
rs4955797	0.87[ASN][1000 genomes]
rs4955799	0.87[ASN][1000 genomes]
rs57935620	0.84[EUR][1000 genomes]
rs61179484	0.93[EUR][1000 genomes]
rs61626196	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6443608	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6761999	0.87[ASN][1000 genomes]
rs6778195	0.85[ASN][1000 genomes]
rs6780631	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6794243	0.86[ASN][1000 genomes]
rs6794279	0.93[EUR][1000 genomes]
rs6797848	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611854	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7638121	0.84[EUR][1000 genomes]
rs9815772	0.87[ASN][1000 genomes]
rs9816837	0.87[ASN][1000 genomes]
rs9832291	0.85[ASN][1000 genomes]
rs9841497	0.84[ASN][1000 genomes]
rs9862902	0.86[ASN][1000 genomes]
rs9871126	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1010148	chr3:178650949-178691377	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178666000-178677800	Weak transcription	HSMMtube	muscle
2	chr3:178668800-178683000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:178669400-178685000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:178671400-178684000	Weak transcription	Primary T cells from cord blood	blood
5	chr3:178673800-178678000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:178676000-178677800	Weak transcription	HSMM	muscle
7	chr3:178676800-178683600	Weak transcription	GM12878-XiMat	blood
8	chr3:178677200-178678600	Enhancers	HUES64 Cell Line	embryonic stem cell

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