Variant report

Variant	rs2622307
Chromosome Location	chr6:64152049-64152050
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10755410	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10806206	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10943902	0.83[JPT][hapmap]
rs1197902	0.83[JPT][hapmap]
rs1197905	0.83[JPT][hapmap]
rs12196062	0.81[ASN][1000 genomes]
rs1322415	0.84[JPT][hapmap]
rs1322416	0.83[JPT][hapmap]
rs1570315	0.84[JPT][hapmap]
rs1620671	0.83[JPT][hapmap]
rs1630182	0.83[JPT][hapmap]
rs1681942	0.83[JPT][hapmap]
rs1681946	0.83[JPT][hapmap]
rs1681947	0.83[JPT][hapmap]
rs1681957	0.83[JPT][hapmap]
rs1723535	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1741801	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1744147	0.87[JPT][hapmap]
rs1744152	0.83[JPT][hapmap]
rs1779747	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1779748	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1969717	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2096346	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146149	0.83[JPT][hapmap]
rs2146150	0.83[JPT][hapmap]
rs2186011	0.81[ASN][1000 genomes]
rs2622274	0.83[JPT][hapmap]
rs2622281	0.83[JPT][hapmap]
rs2622286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2753062	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2753066	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758224	0.83[JPT][hapmap]
rs2758225	0.83[JPT][hapmap]
rs2758237	0.84[JPT][hapmap]
rs2758259	0.83[JPT][hapmap]
rs2800017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800018	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800023	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800027	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800028	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2800048	0.82[JPT][hapmap]
rs2800049	0.84[JPT][hapmap]
rs4358600	0.82[CEU][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4445042	0.81[EUR][1000 genomes]
rs4543353	0.83[JPT][hapmap]
rs4710254	0.81[EUR][1000 genomes]
rs4710255	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4710430	0.82[ASN][1000 genomes]
rs6919709	0.81[EUR][1000 genomes]
rs6929702	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6938965	0.83[JPT][hapmap]
rs6939983	0.81[ASN][1000 genomes]
rs7742595	0.84[ASN][1000 genomes]
rs7745873	0.82[ASN][1000 genomes]
rs7763834	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9294196	0.81[EUR][1000 genomes]
rs9294197	0.81[EUR][1000 genomes]
rs9294198	0.81[EUR][1000 genomes]
rs9294206	0.81[EUR][1000 genomes]
rs9294215	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9294234	0.83[JPT][hapmap]
rs9294269	0.83[JPT][hapmap]
rs9341841	0.81[EUR][1000 genomes]
rs9344090	0.81[EUR][1000 genomes]
rs9344129	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344137	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344168	0.81[ASN][1000 genomes]
rs9350913	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9352960	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9353016	0.82[JPT][hapmap]
rs9359467	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9361762	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9361767	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9361779	0.84[ASN][1000 genomes]
rs9361838	0.83[JPT][hapmap]
rs9449233	0.81[EUR][1000 genomes]
rs9449291	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs9449297	0.82[ASN][1000 genomes]
rs9449312	0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019831	chr6:63279677-64230736	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2622307	LGSN	cis	Whole Blood	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64146600-64158000	Weak transcription	Hela-S3	cervix
2	chr6:64149400-64152400	Active TSS	A549	lung
3	chr6:64149600-64152400	Enhancers	HepG2	liver
4	chr6:64150800-64152400	Active TSS	Placenta	Placenta
5	chr6:64151200-64152200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:64151200-64152200	Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr6:64151200-64152400	Active TSS	K562	blood
8	chr6:64151400-64152200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:64151400-64152200	Active TSS	Primary T cells from cord blood	blood
10	chr6:64151400-64152200	Active TSS	Primary hematopoietic stem cells	blood
11	chr6:64151400-64152200	Active TSS	Fetal Thymus	thymus
12	chr6:64151400-64152200	Active TSS	Thymus	Thymus
13	chr6:64151600-64152200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
14	chr6:64151600-64152200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:64151800-64152200	Active TSS	Primary B cells from cord blood	blood
16	chr6:64151800-64152200	Active TSS	Primary T cells fromperipheralblood	blood
17	chr6:64151800-64152200	Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr6:64151800-64152200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:64152000-64152800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:64152000-64153200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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