Variant report

Variant	rs2343590
Chromosome Location	chr6:166759622-166759623
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10806847	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10862	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4470829	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4598048	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4709112	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6909951	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6918901	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6927168	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7757549	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9355572	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9356476	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9356478	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9356479	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9366005	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9366006	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9366007	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9459654	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2343590	SFT2D1	Cis_1M	lymphoblastoid	RTeQTL
rs2343590	SFT2D1	cis	Whole Blood	GTEx
rs2343590	HNRNPA1P49	cis	lung	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166757000-166765200	Weak transcription	Brain Hippocampus Middle	brain
2	chr6:166757000-166765400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:166757000-166779200	Weak transcription	Right Atrium	heart
4	chr6:166757200-166760000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:166757200-166761000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:166757400-166759800	Weak transcription	Liver	Liver
7	chr6:166757400-166760000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr6:166757400-166760400	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr6:166757400-166762600	Enhancers	HepG2	liver
10	chr6:166757600-166759800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr6:166758600-166760000	Weak transcription	Placenta	Placenta
12	chr6:166759400-166760000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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