Variant report

Variant	rs11162436
Chromosome Location	chr1:78703306-78703307
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10493608	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs10873967	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11162435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323096	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1323097	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323098	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1323099	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1745624	0.89[JPT][hapmap]
rs2181453	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2351912	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4650620	0.86[CEU][hapmap]
rs4650639	0.81[ASN][1000 genomes]
rs589683	0.89[ASN][1000 genomes]
rs591206	0.88[ASN][1000 genomes]
rs646971	0.87[ASN][1000 genomes]
rs648315	0.80[ASN][1000 genomes]
rs6665090	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs666897	0.89[ASN][1000 genomes]
rs679843	0.88[ASN][1000 genomes]
rs681907	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs720579	0.89[ASN][1000 genomes]
rs7540033	0.89[ASN][1000 genomes]
rs942100	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11162436	NEXN	Cis_1M	lymphoblastoid	RTeQTL
rs11162436	LHX8	cis	parietal	SCAN
rs11162436	DNAJB4	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78701800-78703400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:78701800-78703600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr1:78701800-78704000	Enhancers	Gastric	stomach
4	chr1:78701800-78704000	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr1:78702200-78704200	Enhancers	Hela-S3	cervix
6	chr1:78702400-78704000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:78702400-78704000	Enhancers	Liver	Liver
8	chr1:78702400-78704000	Enhancers	HMEC	breast
9	chr1:78702600-78703800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
10	chr1:78702800-78703400	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr1:78702800-78704000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
12	chr1:78702800-78704000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
13	chr1:78702800-78704000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:78702800-78704000	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr1:78702800-78704000	Enhancers	Stomach Mucosa	stomach
16	chr1:78702800-78704200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
17	chr1:78702800-78706000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:78702800-78706200	Weak transcription	Osteobl	bone
19	chr1:78702800-78706400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:78703000-78703800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
21	chr1:78703000-78704000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
22	chr1:78703000-78704000	Enhancers	Pancreas	Pancrea
23	chr1:78703000-78706200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:78703000-78706600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:78703200-78703400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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