Variant report

Variant	rs7540791
Chromosome Location	chr1:222023848-222023849
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222023733..222024287-chr9:100684011..100684780,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000136932	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10863665	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11118877	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12027640	0.86[ASN][1000 genomes]
rs12047353	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12140184	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12144971	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4240931	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4846731	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6604679	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6604680	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6604682	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7540791	AIDA	cis	parietal	SCAN
rs7540791	HHIPL2	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222015600-222024600	Weak transcription	HSMMtube	muscle
2	chr1:222019600-222024400	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:222019800-222024200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:222019800-222024400	Weak transcription	Esophagus	oesophagus
5	chr1:222019800-222024600	Weak transcription	NHLF	lung
6	chr1:222019800-222031800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:222019800-222047600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:222020200-222024400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:222020200-222029600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:222020400-222024000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:222020400-222024200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:222020600-222024400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:222020600-222031600	Weak transcription	HMEC	breast
14	chr1:222023200-222024000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:222023400-222024400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:222023400-222024600	Enhancers	Placenta	Placenta
17	chr1:222023400-222025800	Enhancers	Hela-S3	cervix
18	chr1:222023600-222024000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:222023600-222024200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:222023600-222024400	Weak transcription	HSMM	muscle
21	chr1:222023600-222026000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:222023800-222024600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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