Variant report

Variant	rs7539956
Chromosome Location	chr1:78524194-78524195
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:78444119..78446567-chr1:78523536..78526376,3	K562	blood:
2	chr1:78518422..78519997-chr1:78524033..78526694,2	K562	blood:
3	chr1:78520206..78525011-chr1:78526646..78528908,4	K562	blood:

Variant related genes	Relation type
ENSG00000137960	Chromatin interaction
ENSG00000162613	Chromatin interaction
ENSG00000162616	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11162412	0.82[AMR][1000 genomes]
rs12067638	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5001390	0.80[AMR][1000 genomes]
rs505301	0.82[AMR][1000 genomes]
rs515662	0.80[AMR][1000 genomes]
rs594852	0.82[AMR][1000 genomes]
rs610501	0.82[AMR][1000 genomes]
rs630640	0.81[JPT][hapmap]
rs638668	0.82[AMR][1000 genomes]
rs6424659	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs654185	0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6669039	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs666995	0.82[AMR][1000 genomes]
rs6688346	0.82[AMR][1000 genomes]
rs6702939	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.87[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	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv870608	chr1:78520822-78594286	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7539956	NEXN	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78515400-78534200	Weak transcription	HepG2	liver
2	chr1:78519000-78536000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:78519200-78527000	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:78519800-78526800	Weak transcription	Psoas Muscle	Psoas
5	chr1:78520800-78526600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:78520800-78526800	Weak transcription	HSMMtube	muscle
7	chr1:78521000-78524200	Weak transcription	HSMM	muscle
8	chr1:78521600-78526800	Weak transcription	Fetal Intestine Large	intestine
9	chr1:78521600-78526800	Weak transcription	Right Atrium	heart
10	chr1:78521600-78526800	Weak transcription	HMEC	breast
11	chr1:78521600-78534600	Weak transcription	Colonic Mucosa	Colon
12	chr1:78521800-78525200	Weak transcription	Fetal Intestine Small	intestine
13	chr1:78521800-78526600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:78521800-78526800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:78521800-78526800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:78521800-78526800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:78521800-78527600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:78521800-78527800	Weak transcription	HUVEC	blood vessel
19	chr1:78521800-78534600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:78522000-78524600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:78522000-78524600	Weak transcription	Pancreas	Pancrea
22	chr1:78522000-78527000	Weak transcription	Left Ventricle	heart
23	chr1:78522200-78529800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:78523800-78525400	Enhancers	Osteobl	bone
25	chr1:78524000-78525000	Enhancers	Muscle Satellite Cultured Cells	--

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