Variant report

Variant	rs6550819
Chromosome Location	chr3:23984133-23984134
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
2	chr3:23930082..23933040-chr3:23982116..23985334,3	K562	blood:
3	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174748	Chromatin interaction
ENSG00000197885	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11717862	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13091509	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13095392	0.89[EUR][1000 genomes]
rs4025822	0.83[EUR][1000 genomes]
rs4131403	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4241514	0.86[EUR][1000 genomes]
rs4241515	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4241517	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4241520	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4320034	0.84[AFR][1000 genomes]
rs4321479	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4589882	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4619734	0.91[EUR][1000 genomes]
rs4858094	0.85[EUR][1000 genomes]
rs4858095	0.92[EUR][1000 genomes]
rs4858098	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858551	0.85[EUR][1000 genomes]
rs4858553	0.85[EUR][1000 genomes]
rs4858565	0.86[EUR][1000 genomes]
rs4858567	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858569	0.85[ASN][1000 genomes]
rs62253379	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6419846	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6550814	0.92[ASN][1000 genomes]
rs6550815	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6550823	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6550824	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6764154	0.85[EUR][1000 genomes]
rs6779476	0.92[EUR][1000 genomes]
rs6790557	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6793391	0.82[AFR][1000 genomes]
rs6794922	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7371944	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7431301	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7636810	0.90[ASN][1000 genomes]
rs9845287	0.85[EUR][1000 genomes]
rs9853532	0.88[ASN][1000 genomes]
rs9863320	0.83[EUR][1000 genomes]
rs9882735	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv3341907	chr3:23984076-23984451	Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23962000-23985600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr3:23964200-23985000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr3:23976800-23985600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:23979000-23985200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:23979000-23985400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:23979200-23985600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:23980400-23985200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:23980400-23985800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:23980600-23985200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:23980600-23985200	Weak transcription	Fetal Lung	lung
11	chr3:23980800-23985200	Weak transcription	Fetal Heart	heart
12	chr3:23982200-23986000	Weak transcription	Right Atrium	heart
13	chr3:23983200-23985200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:23983400-23985200	Weak transcription	K562	blood

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