Variant report

Variant	rs6663154
Chromosome Location	chr1:224246746-224246747
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12725040	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12725830	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12731770	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs16848126	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34387992	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34978219	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35533869	0.86[ASN][1000 genomes]
rs57408556	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7536577	0.93[AMR][1000 genomes];0.90[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	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv427941	chr1:224085052-224363163	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv511736	chr1:224245309-224248054	Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2434057	chr1:224246472-224248330	Weak transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6663154	MIA3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224244400-224247000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:224244800-224248000	Enhancers	HUVEC	blood vessel
3	chr1:224245000-224246800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:224245000-224247000	Enhancers	HMEC	breast
5	chr1:224245400-224246800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:224245600-224250600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:224245800-224247600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:224245800-224247800	Weak transcription	K562	blood
9	chr1:224245800-224249200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:224245800-224251000	Weak transcription	Fetal Intestine Large	intestine
11	chr1:224245800-224251400	Weak transcription	Stomach Mucosa	stomach
12	chr1:224246000-224246800	Enhancers	NHEK	skin
13	chr1:224246400-224248600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:224246400-224253400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:224246600-224251400	Weak transcription	Gastric	stomach

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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