Variant report

Variant	rs6688484
Chromosome Location	chr1:186744376-186744377
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLA2G4A-8	chr1:186744292-186744419	NONHSAT008452

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10489402	1.00[ASN][1000 genomes]
rs10489403	1.00[ASN][1000 genomes]
rs10489404	1.00[ASN][1000 genomes]
rs10489405	1.00[ASN][1000 genomes]
rs10737269	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10752971	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10752973	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10752974	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10798055	0.91[EUR][1000 genomes]
rs10798057	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10911922	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1158042	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1158043	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12029765	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12116711	0.85[EUR][1000 genomes]
rs12117451	0.89[EUR][1000 genomes]
rs12119919	0.89[EUR][1000 genomes]
rs12144220	0.89[EUR][1000 genomes]
rs12239319	1.00[ASN][1000 genomes]
rs12239469	1.00[ASN][1000 genomes]
rs12239842	1.00[ASN][1000 genomes]
rs13374461	1.00[ASN][1000 genomes]
rs13375208	1.00[ASN][1000 genomes]
rs13375339	1.00[ASN][1000 genomes]
rs16825875	1.00[ASN][1000 genomes]
rs16825907	1.00[ASN][1000 genomes]
rs16825911	1.00[ASN][1000 genomes]
rs16825962	1.00[ASN][1000 genomes]
rs1980454	0.98[EUR][1000 genomes]
rs2205951	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2223329	0.92[EUR][1000 genomes]
rs2223330	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650701	0.92[EUR][1000 genomes]
rs6425049	0.98[EUR][1000 genomes]
rs6656505	1.00[ASN][1000 genomes]
rs6660635	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6663605	1.00[EUR][1000 genomes]
rs6692679	0.98[EUR][1000 genomes]
rs7418312	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7515232	1.00[ASN][1000 genomes]
rs7516460	0.98[EUR][1000 genomes]
rs7523981	0.89[EUR][1000 genomes]
rs7532307	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7554410	0.98[EUR][1000 genomes]
rs7555275	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs766400	0.91[EUR][1000 genomes]
rs964570	0.91[EUR][1000 genomes]
rs9970503	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv2762854	chr1:186547101-186847574	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv872590	chr1:186557453-187500338	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv466272	chr1:186742947-186803226	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv548406	chr1:186742947-186803226	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186741400-186745200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:186743400-186745400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:186743400-186745600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:186743600-186744400	Enhancers	Rectal Smooth Muscle	rectum
5	chr1:186743800-186745400	Enhancers	Fetal Lung	lung

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