Variant report

Variant	rs6424660
Chromosome Location	chr1:78501604-78501605
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:78466509..78474870-chr1:78497253..78506543,20	K562	blood:
2	chr1:78500187..78503737-chr1:78504234..78506464,4	K562	blood:
3	chr1:78490302..78495506-chr1:78500007..78505511,6	K562	blood:

Variant related genes	Relation type
ENSG00000273338	Chromatin interaction
ENSG00000162616	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1001070	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1001103	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1001104	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10437022	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10873960	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10873962	0.86[AMR][1000 genomes]
rs10873963	0.95[AMR][1000 genomes]
rs11162400	0.80[AMR][1000 genomes]
rs11162403	0.90[AMR][1000 genomes]
rs11162406	0.87[AMR][1000 genomes]
rs1166697	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1166701	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1166702	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1166704	0.82[AMR][1000 genomes]
rs1166707	0.82[AMR][1000 genomes]
rs11805735	0.84[AMR][1000 genomes]
rs11807240	0.84[AMR][1000 genomes]
rs12146104	0.82[AMR][1000 genomes]
rs12405212	0.84[AMR][1000 genomes]
rs12409561	0.84[AMR][1000 genomes]
rs1335481	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1536160	0.84[AMR][1000 genomes]
rs1555798	0.80[AMR][1000 genomes]
rs1616949	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1855704	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1971368	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2136682	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2274257	0.80[AMR][1000 genomes]
rs2296453	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3767028	0.84[AMR][1000 genomes]
rs4370803	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4372306	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs4631748	0.95[AMR][1000 genomes]
rs4949828	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4949829	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs5001389	0.85[ASN][1000 genomes]
rs504388	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs568497	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs57421725	0.84[AMR][1000 genomes]
rs628451	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs638335	0.85[ASN][1000 genomes]
rs6424640	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6424650	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6424664	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6424668	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs661038	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs662330	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs664818	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6656888	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6677890	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6686230	0.86[AMR][1000 genomes]
rs684579	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs750720	0.84[AMR][1000 genomes]
rs7514007	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7538210	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9324166	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9659938	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9661193	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9730688	0.88[AMR][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	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78485000-78504000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:78485400-78504200	Weak transcription	NH-A	brain
3	chr1:78486400-78509400	Weak transcription	HSMM	muscle
4	chr1:78499400-78503600	Weak transcription	Hela-S3	cervix
5	chr1:78499400-78503800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:78499400-78509200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr1:78499600-78505000	Weak transcription	Pancreas	Pancrea
8	chr1:78499600-78509200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:78500000-78503800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:78500200-78506600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:78501400-78503800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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