Variant report

Variant	rs6561776
Chromosome Location	chr13:55015561-55015562
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:55015549-55015599	AG09309	skin:	n/a
2	chr13:55015549-55015599	Hela-S3	cervix:	n/a
3	chr13:55015549-55015599	HRCEpiC	kidney:	n/a
4	chr13:55015549-55015599	SK-N-MC	brain:	n/a
5	chr13:55015549-55015599	K562	blood:	n/a
6	chr13:55015549-55015599	H1-hESC	embryonic stem cell:	embryo
7	chr13:55015549-55015599	RPTEC	kidney:	n/a
8	chr13:55015549-55015599	HEEpiC	esophagus:	n/a
9	chr13:55015549-55015599	AG10803	skin:	n/a
10	chr13:55015549-55015599	T-47D	breast:	n/a
11	chr13:55015549-55015599	NB4	blood:	n/a
12	chr13:55015549-55015599	SKMC	muscle:	n/a
13	chr13:55015549-55015599	U87	brain:	n/a
14	chr13:55015549-55015599	SAEC	small airway:	n/a
15	chr13:55015549-55015599	HRE	kidney:	n/a
16	chr13:55015549-55015599	HUVEC	blood vessel:	n/a
17	chr13:55015549-55015599	GM12878	blood:	n/a
18	chr13:55015549-55015599	Jurkat	blood:	n/a
19	chr13:55015549-55015599	HRPEpiC	eye:	n/a
20	chr13:55015549-55015599	NH-A	brain:	n/a
21	chr13:55015549-55015599	HPAEpiC	pulmonary alveolar:	n/a
22	chr13:55015549-55015599	BJ	skin:	n/a
23	chr13:55015549-55015599	MCF-7	breast:	n/a
24	chr13:55015549-55015599	SK-N-SH_RA	brain:	n/a
25	chr13:55015549-55015599	GM12891	blood:	n/a
26	chr13:55015549-55015599	AG09319	gingival:	n/a
27	chr13:55015549-55015599	ECC-1	luminal epithelium:	n/a
28	chr13:55015549-55015599	HEK293	kidney:	embryo
29	chr13:55015549-55015599	HCF	heart:	n/a
30	chr13:55015549-55015599	NHBE	bronchial:	n/a
31	chr13:55015549-55015599	CMK	blood:	n/a
32	chr13:55015549-55015599	HL-60	blood:	n/a
33	chr13:55015549-55015599	GM19239	blood:	n/a
34	chr13:55015549-55015599	AG04449	skin:	fetal
35	chr13:55015549-55015599	GM12892	blood:	n/a
36	chr13:55015549-55015599	HCPEpiC	choroid plexus:	n/a
37	chr13:55015549-55015599	NHDF-neo	bronchial:	n/a
38	chr13:55015549-55015599	PrEC	prostate:	n/a
39	chr13:55015549-55015599	HCT-116	colon:	n/a
40	chr13:55015549-55015599	AoSMC	blood vessel:	n/a
41	chr13:55015549-55015599	MCF10A-Er-Src	breast:	n/a
42	chr13:55015549-55015599	PFSK-1	brain:	n/a
43	chr13:55015549-55015599	Caco-2	colon:	n/a
44	chr13:55015549-55015599	GM06990	blood:	n/a
45	chr13:55015549-55015599	HMEC	breast:	n/a
46	chr13:55015549-55015599	PANC-1	pancreas:	n/a
47	chr13:55015549-55015599	HIPEpiC	eye:	n/a
48	chr13:55015549-55015599	BE2_C	brain:	n/a
49	chr13:55015549-55015599	AG04450	lung:	fetal
50	chr13:55015549-55015599	A549	lung:	n/a

No data

Variant related genes	Relation type
RPL13AP25	CpG island

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10047802	0.85[ASN][1000 genomes]
rs13378130	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28510486	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34883109	0.85[ASN][1000 genomes]
rs35451065	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61954782	0.85[ASN][1000 genomes]
rs61954783	0.85[ASN][1000 genomes]
rs61954784	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73201621	0.88[ASN][1000 genomes]
rs73201626	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7322728	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7335700	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8001623	0.85[ASN][1000 genomes]
rs9591590	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9591591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9591592	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs9596952	0.85[ASN][1000 genomes]
rs9596953	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9596954	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9596955	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9805180	0.85[ASN][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	esv3349795	chr13:54892694-55252030	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2763025	chr13:55004448-55023333	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
3	nsv977246	chr13:55013586-55019919	Weak transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
4	esv3344823	chr13:55013801-55015749	Weak transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6561776	LECT1	cis	parietal	SCAN
rs6561776	LECT1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:55012200-55016200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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