Variant report

Variant	rs4801877
Chromosome Location	chr19:39265241-39265242
allele	C/T
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:1)
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	chr19:39265241-39265291	HCF	heart:	n/a
2	chr19:39265241-39265291	HEK293	kidney:	embryo
3	chr19:39265241-39265291	MCF10A-Er-Src	breast:	n/a
4	chr19:39265241-39265291	HUVEC	blood vessel:	n/a
5	chr19:39265241-39265291	ProgFib	skin:	n/a
6	chr19:39265241-39265291	Hepatocyte	liver:	n/a
7	chr19:39265241-39265291	RPTEC	kidney:	n/a
8	chr19:39265241-39265291	SK-N-SH	brain:	n/a
9	chr19:39265241-39265291	GM19239	blood:	n/a
10	chr19:39265241-39265291	HIPEpiC	eye:	n/a
11	chr19:39265241-39265291	Caco-2	colon:	n/a
12	chr19:39265241-39265291	NT2-D1	testis:	n/a
13	chr19:39265241-39265291	Hela-S3	cervix:	n/a
14	chr19:39265241-39265291	HRE	kidney:	n/a
15	chr19:39265241-39265291	SK-N-MC	brain:	n/a
16	chr19:39265241-39265291	PrEC	prostate:	n/a
17	chr19:39265241-39265291	AG09319	gingival:	n/a
18	chr19:39265241-39265291	IMR90	lung:	fetal
19	chr19:39265241-39265291	AoSMC	blood vessel:	n/a
20	chr19:39265241-39265291	SAEC	small airway:	n/a
21	chr19:39265241-39265291	HMEC	breast:	n/a
22	chr19:39265241-39265291	SK-N-SH_RA	brain:	n/a
23	chr19:39265241-39265291	NH-A	brain:	n/a
24	chr19:39265241-39265291	HCPEpiC	choroid plexus:	n/a
25	chr19:39265241-39265291	U87	brain:	n/a
26	chr19:39265241-39265291	HAEpiC	amniotic membrane:	n/a
27	chr19:39265241-39265291	AG10803	skin:	n/a
28	chr19:39265241-39265291	PFSK-1	brain:	n/a
29	chr19:39265241-39265291	K562	blood:	n/a
30	chr19:39265241-39265291	GM12891	blood:	n/a
31	chr19:39265241-39265291	HepG2	liver:	n/a
32	chr19:39265241-39265291	NB4	blood:	n/a
33	chr19:39265241-39265291	PANC-1	pancreas:	n/a
34	chr19:39265241-39265291	MCF-7	breast:	n/a
35	chr19:39265241-39265291	ovcar-3	ovarian:	n/a
36	chr19:39265241-39265291	HCM	heart:	n/a
37	chr19:39265241-39265291	CMK	blood:	n/a
38	chr19:39265241-39265291	T-47D	breast:	n/a
39	chr19:39265241-39265291	HPAEpiC	pulmonary alveolar:	n/a
40	chr19:39265241-39265291	ECC-1	luminal epithelium:	n/a
41	chr19:39265241-39265291	HNPCEpiC	eye:	n/a
42	chr19:39265241-39265291	GM12878	blood:	n/a
43	chr19:39265241-39265291	AG04449	skin:	fetal
44	chr19:39265241-39265291	GM12892	blood:	n/a
45	chr19:39265241-39265291	HEEpiC	esophagus:	n/a
46	chr19:39265241-39265291	A549	lung:	n/a
47	chr19:39265241-39265291	AG04450	lung:	fetal
48	chr19:39265241-39265291	LNCaP	prostate:	n/a
49	chr19:39265241-39265291	HL-60	blood:	n/a
50	chr19:39265241-39265291	HCT-116	colon:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39264503..39266421-chr19:39288858..39290428,2	MCF-7	breast:

No data

Variant related genes	Relation type
LGALS7	CpG island
CAPN12	CpG island

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10410924	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10411352	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10422547	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10422733	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10423065	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10424200	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10424620	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11667079	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11669239	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2001274	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55647604	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56265037	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs57217905	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58406458	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60800281	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7246893	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7247185	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7247475	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8108412	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8109475	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8109993	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8110778	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8111887	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8112427	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9749397	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9749398	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv1064688	chr19:39249059-39291526	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv1061904	chr19:39249692-39302843	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
6	nsv911670	chr19:39250308-39322087	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv911671	chr19:39252238-39306425	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
8	nsv911672	chr19:39252238-39318006	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1063592	chr19:39257977-39287265	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4801877	LGALS7	cis	Esophagus Mucosa	GTEx
rs4801877	RNU6-140P	cis	Esophagus Mucosa	GTEx
rs4801877	CAPN12	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39246400-39270800	Weak transcription	K562	blood
2	chr19:39254200-39265400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:39261000-39265400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr19:39261000-39269400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:39262200-39274800	Weak transcription	Fetal Intestine Large	intestine
6	chr19:39264200-39266200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:39264200-39266400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr19:39264200-39266400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr19:39264200-39266600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:39264200-39266600	Enhancers	HMEC	breast
11	chr19:39264200-39266600	Enhancers	NHEK	skin
12	chr19:39264600-39265600	Enhancers	Spleen	Spleen
13	chr19:39264600-39265800	Enhancers	Stomach Mucosa	stomach
14	chr19:39264600-39266200	Enhancers	Esophagus	oesophagus
15	chr19:39264800-39266000	Weak transcription	A549	lung
16	chr19:39264800-39274800	Weak transcription	Fetal Intestine Small	intestine
17	chr19:39265000-39265400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr19:39265000-39267800	Weak transcription	HepG2	liver
19	chr19:39265200-39265400	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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