Variant report

Variant	rs539228
Chromosome Location	chr1:78556177-78556178
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:78556113-78556698	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr1:78556098-78556667	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr1:78556075-78556678	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr1:78556130-78556661	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:78472783..78474858-chr1:78555582..78557141,2	K562	blood:
2	chr1:78468129..78475881-chr1:78555411..78565499,18	K562	blood:
3	chr1:78555766..78558771-chr1:78559495..78562438,3	K562	blood:
4	chr1:78467305..78472459-chr1:78554681..78560615,12	K562	blood:

Variant related genes	Relation type
ENSG00000213560	TF binding region
RNU6-1102P	TF binding region
ENSG00000202263	Chromatin interaction
ENSG00000273338	Chromatin interaction
ENSG00000162616	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];0.92[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];0.98[ASN][1000 genomes]
rs481199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs483760	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs485005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5001390	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs501935	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs505301	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs515662	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs565164	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];0.93[ASN][1000 genomes]
rs571988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586680	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs587143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs594852	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs598988	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs600742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs610501	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs611820	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs630245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs630640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs638668	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs639677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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];0.99[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];0.93[ASN][1000 genomes]
rs658780	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs664448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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];0.92[ASN][1000 genomes]
rs6688346	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs677640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs686716	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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
rs539228	NEXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 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	chr1:78544200-78556400	Weak transcription	K562	blood
3	chr1:78544200-78558200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:78545400-78561800	Weak transcription	Left Ventricle	heart
5	chr1:78545400-78562600	Weak transcription	Small Intestine	intestine
6	chr1:78546600-78579800	Weak transcription	Liver	Liver
7	chr1:78546800-78561400	Weak transcription	Ovary	ovary
8	chr1:78549600-78560200	Weak transcription	Fetal Heart	heart
9	chr1:78550800-78562600	Weak transcription	Aorta	Aorta
10	chr1:78553400-78567000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:78553600-78557000	Weak transcription	Right Ventricle	heart
12	chr1:78554400-78556400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:78554600-78557200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:78554800-78558400	Weak transcription	HUVEC	blood vessel
15	chr1:78554800-78579800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:78555000-78560400	Weak transcription	Osteobl	bone
17	chr1:78555000-78563000	Weak transcription	HepG2	liver
18	chr1:78555400-78556400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:78555400-78557000	Weak transcription	Fetal Intestine Large	intestine
20	chr1:78555400-78557000	Weak transcription	Fetal Intestine Small	intestine
21	chr1:78555400-78608600	Weak transcription	Pancreas	Pancrea

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