Variant report

Variant	rs565164
Chromosome Location	chr1:78560583-78560584
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:78555766..78558771-chr1:78559495..78562438,3	K562	blood:
2	chr1:78468129..78475881-chr1:78555411..78565499,18	K562	blood:
3	chr1:78467305..78472459-chr1:78554681..78560615,12	K562	blood:

Variant related genes	Relation type
ENSG00000273338	Chromatin interaction
ENSG00000162616	Chromatin interaction
ENSG00000213560	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11162412	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12067638	0.91[AFR][1000 genomes]
rs3790592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs481199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs483760	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs485005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5001390	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs501935	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs505301	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs515662	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs539228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs571255	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs571988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs586680	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs587143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs594852	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs598988	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs600742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs610501	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs611820	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs630245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs630640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs638668	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs639677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs640935	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs643512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs654185	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs657954	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs658780	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs664448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6669039	0.94[AFR][1000 genomes]
rs666995	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6688346	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs677640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs686716	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs812097	0.90[AFR][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	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
5	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs565164	NEXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78535000-78566800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:78545400-78561800	Weak transcription	Left Ventricle	heart
3	chr1:78545400-78562600	Weak transcription	Small Intestine	intestine
4	chr1:78546600-78579800	Weak transcription	Liver	Liver
5	chr1:78546800-78561400	Weak transcription	Ovary	ovary
6	chr1:78550800-78562600	Weak transcription	Aorta	Aorta
7	chr1:78553400-78567000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:78554800-78579800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:78555000-78563000	Weak transcription	HepG2	liver
10	chr1:78555400-78608600	Weak transcription	Pancreas	Pancrea
11	chr1:78556600-78560800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:78556600-78560800	Weak transcription	NHLF	lung
13	chr1:78557400-78561600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:78557800-78562400	Weak transcription	Right Ventricle	heart
15	chr1:78557800-78569200	Weak transcription	Fetal Intestine Small	intestine
16	chr1:78558000-78561000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr1:78558200-78562400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:78558400-78561200	Enhancers	HUVEC	blood vessel
19	chr1:78558600-78582800	Weak transcription	Fetal Intestine Large	intestine
20	chr1:78558800-78560600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:78558800-78560600	Weak transcription	NHDF-Ad	bronchial
22	chr1:78559400-78563400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:78559600-78560600	Weak transcription	HMEC	breast
24	chr1:78559600-78560600	Weak transcription	NHEK	skin
25	chr1:78559800-78561200	Enhancers	Brain Anterior Caudate	brain
26	chr1:78559800-78561400	Weak transcription	Hela-S3	cervix
27	chr1:78559800-78563800	Enhancers	HSMMtube	muscle
28	chr1:78560000-78560800	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:78560200-78561200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:78560200-78563200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:78560200-78563400	Enhancers	Fetal Heart	heart
32	chr1:78560200-78563600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:78560200-78563600	Enhancers	Brain Substantia Nigra	brain
34	chr1:78560400-78560600	Enhancers	K562	blood
35	chr1:78560400-78561000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr1:78560400-78561000	Flanking Active TSS	HSMM	muscle
37	chr1:78560400-78561400	Weak transcription	Right Atrium	heart
38	chr1:78560400-78563600	Enhancers	Osteobl	bone

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