Variant report

Variant	rs6657216
Chromosome Location	chr1:85492386-85492387
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11800303	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11807839	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11808352	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56254105	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56973472	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57386218	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59019108	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60296374	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74095725	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74095727	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74095734	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74095735	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74095737	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74095739	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7545349	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7546496	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7551619	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6657216	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85483600-85494800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:85485400-85513000	Weak transcription	Pancreas	Pancrea
3	chr1:85485800-85505200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr1:85486000-85513000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:85486400-85499200	Weak transcription	NHDF-Ad	bronchial
6	chr1:85486400-85500400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:85488000-85493000	Weak transcription	HMEC	breast
8	chr1:85488800-85493000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:85489000-85492600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr1:85489000-85492600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:85489000-85500000	Weak transcription	Adipose Nuclei	Adipose
12	chr1:85490600-85492800	Weak transcription	GM12878-XiMat	blood
13	chr1:85490800-85494400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:85491400-85493000	Weak transcription	Fetal Intestine Large	intestine
15	chr1:85492200-85497000	Strong transcription	Fetal Intestine Small	intestine

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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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