Variant report

Variant	rs392077
Chromosome Location	chr5:41264328-41264329
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	EP300	chr5:41263799-41264537	SK-N-SH_RA	brain:	n/a	n/a
2	GATA3	chr5:41263876-41264691	SK-N-SH	brain:	n/a	chr5:41264225-41264235 chr5:41264214-41264231
3	NFIC	chr5:41263880-41264665	SK-N-SH	brain:	n/a	n/a
4	YY1	chr5:41264124-41264472	SK-N-SH_RA	brain:	n/a	n/a
5	TCF12	chr5:41263824-41264689	SK-N-SH	brain:	n/a	n/a
6	EP300	chr5:41263836-41264563	SK-N-SH	brain:	n/a	n/a
7	RAD21	chr5:41263897-41264506	SK-N-SH_RA	brain:	n/a	n/a
8	TCF12	chr5:41263900-41264640	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr5:41264092-41264395	SK-N-SH	brain:	n/a	n/a
10	TEAD4	chr5:41263923-41264626	SK-N-SH	brain:	n/a	n/a
11	EP300	chr5:41261904-41266906	SK-N-SH	brain:	n/a	chr5:41262545-41262559 chr5:41265238-41265252 chr5:41265254-41265268 chr5:41262584-41262593 chr5:41265714-41265724 chr5:41265664-41265678 chr5:41265765-41265778
12	GATA2	chr5:41263871-41265105	SH-SY5Y	brain:	n/a	chr5:41264225-41264235 chr5:41264936-41264943 chr5:41264214-41264231
13	GATA3	chr5:41263884-41264634	SK-N-SH	brain:	n/a	chr5:41264225-41264235 chr5:41264214-41264231
14	EP300	chr5:41263876-41264597	SK-N-SH_RA	brain:	n/a	n/a
15	POLR2A	chr5:41264007-41264490	SK-N-SH	brain:	n/a	n/a
16	GATA3	chr5:41263920-41264503	SH-SY5Y	brain:	n/a	chr5:41264225-41264235 chr5:41264214-41264231
17	RAD21	chr5:41264088-41264507	SK-N-SH_RA	brain:	n/a	n/a
18	JUND	chr5:41263988-41264471	SK-N-SH	brain:	n/a	chr5:41264386-41264397
19	TEAD4	chr5:41263935-41264495	SK-N-SH	brain:	n/a	n/a
20	PBX3	chr5:41263993-41264451	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
C6	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs2910644	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs2921178	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs364539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs380649	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs390035	0.95[ASN][1000 genomes]
rs399661	0.97[ASN][1000 genomes]
rs399760	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs412685	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418697	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420448	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422027	0.93[ASN][1000 genomes]
rs429017	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs433072	0.97[ASN][1000 genomes]
rs433224	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427717	chr5:41201377-41369202	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv830269	chr5:41209113-41393536	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs392077	LIFR	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41263000-41264400	Enhancers	Fetal Heart	heart
2	chr5:41263200-41265000	Enhancers	Duodenum Mucosa	Duodenum
3	chr5:41263200-41265000	Enhancers	Fetal Intestine Large	intestine
4	chr5:41263200-41265000	Enhancers	Fetal Lung	lung
5	chr5:41263400-41264800	Enhancers	Adipose Nuclei	Adipose
6	chr5:41263400-41264800	Enhancers	Stomach Mucosa	stomach
7	chr5:41263400-41266800	Enhancers	Fetal Intestine Small	intestine
8	chr5:41263600-41264800	Enhancers	Right Atrium	heart
9	chr5:41263800-41264400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:41263800-41264400	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr5:41263800-41264600	Enhancers	Right Ventricle	heart
12	chr5:41264000-41267600	Weak transcription	Ovary	ovary
13	chr5:41264200-41264600	Enhancers	Fetal Muscle Leg	muscle
14	chr5:41264200-41265600	Enhancers	Small Intestine	intestine

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