Variant report

Variant	rs4802853
Chromosome Location	chr19:39279713-39279714
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr19:39279667-39279863	HepG2	liver:	n/a	chr19:39279780-39279789 chr19:39279781-39279788 chr19:39279779-39279789 chr19:39279778-39279790 chr19:39279779-39279788
2	FOSL2	chr19:39279664-39279871	HepG2	liver:	n/a	chr19:39279780-39279789 chr19:39279781-39279788 chr19:39279779-39279789 chr19:39279778-39279790 chr19:39279665-39279676 chr19:39279779-39279788

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:39279703-39279753	NH-A	brain:	n/a
2	chr19:39279703-39279753	SK-N-MC	brain:	n/a
3	chr19:39279703-39279753	GM12878	blood:	n/a
4	chr19:39279703-39279753	SKMC	muscle:	n/a
5	chr19:39279703-39279753	Caco-2	colon:	n/a
6	chr19:39279703-39279753	GM06990	blood:	n/a
7	chr19:39279703-39279753	LNCaP	prostate:	n/a
8	chr19:39279703-39279753	GM19239	blood:	n/a
9	chr19:39279703-39279753	HIPEpiC	eye:	n/a
10	chr19:39279703-39279753	SK-N-SH_RA	brain:	n/a
11	chr19:39279703-39279753	U87	brain:	n/a
12	chr19:39279703-39279753	Hela-S3	cervix:	n/a
13	chr19:39279703-39279753	MCF10A-Er-Src	breast:	n/a
14	chr19:39279703-39279753	T-47D	breast:	n/a
15	chr19:39279703-39279753	PANC-1	pancreas:	n/a
16	chr19:39279703-39279753	NHBE	bronchial:	n/a
17	chr19:39279703-39279753	SAEC	small airway:	n/a
18	chr19:39279703-39279753	PrEC	prostate:	n/a
19	chr19:39279703-39279753	HEEpiC	esophagus:	n/a
20	chr19:39279703-39279753	HCPEpiC	choroid plexus:	n/a
21	chr19:39279703-39279753	GM12892	blood:	n/a
22	chr19:39279703-39279753	HAEpiC	amniotic membrane:	n/a
23	chr19:39279703-39279753	AG09319	gingival:	n/a
24	chr19:39279703-39279753	HCF	heart:	n/a
25	chr19:39279703-39279753	HCT-116	colon:	n/a
26	chr19:39279703-39279753	Hepatocyte	liver:	n/a
27	chr19:39279703-39279753	NHDF-neo	bronchial:	n/a
28	chr19:39279703-39279753	AoSMC	blood vessel:	n/a
29	chr19:39279703-39279753	NB4	blood:	n/a
30	chr19:39279703-39279753	ProgFib	skin:	n/a
31	chr19:39279703-39279753	HNPCEpiC	eye:	n/a
32	chr19:39279703-39279753	IMR90	lung:	fetal
33	chr19:39279703-39279753	Jurkat	blood:	n/a
34	chr19:39279703-39279753	H1-hESC	embryonic stem cell:	embryo
35	chr19:39279703-39279753	MCF-7	breast:	n/a
36	chr19:39279703-39279753	HRE	kidney:	n/a
37	chr19:39279703-39279753	SK-N-SH	brain:	n/a
38	chr19:39279703-39279753	BE2_C	brain:	n/a
39	chr19:39279703-39279753	AG10803	skin:	n/a
40	chr19:39279703-39279753	NT2-D1	testis:	n/a
41	chr19:39279703-39279753	A549	lung:	n/a
42	chr19:39279703-39279753	HUVEC	blood vessel:	n/a
43	chr19:39279703-39279753	AG04449	skin:	fetal
44	chr19:39279703-39279753	AG09309	skin:	n/a
45	chr19:39279703-39279753	GM12891	blood:	n/a
46	chr19:39279703-39279753	HRPEpiC	eye:	n/a
47	chr19:39279703-39279753	AG04450	lung:	fetal
48	chr19:39279703-39279753	K562	blood:	n/a
49	chr19:39279703-39279753	HCM	heart:	n/a
50	chr19:39279703-39279753	BJ	skin:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39278557..39281313-chr19:39305805..39307829,2	MCF-7	breast:

No data

Variant related genes	Relation type
LGALS7B	TF binding region
LGALS7B	CpG island
ENSG00000104823	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10403583	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10422360	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11667149	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11670444	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11671359	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35116302	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4802817	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6508817	0.88[ASN][1000 genomes]
rs7255094	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7259749	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8108748	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8111466	0.85[ASN][1000 genomes]
rs974454	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
10	nsv9720	chr19:39277331-39283376	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
11	nsv1058132	chr19:39279522-39302843	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4802853	LGALS7	cis	Esophagus Mucosa	GTEx
rs4802853	CAPN12	cis	Heart Left Ventricle	GTEx
rs4802853	LGALS7	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39265600-39283000	Weak transcription	Spleen	Spleen
2	chr19:39276200-39283000	Weak transcription	Pancreas	Pancrea
3	chr19:39277200-39283200	Weak transcription	NH-A	brain
4	chr19:39277800-39282800	Weak transcription	Placenta	Placenta
5	chr19:39277800-39283000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr19:39277800-39283000	Weak transcription	Right Ventricle	heart
7	chr19:39278000-39283000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr19:39278600-39279800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr19:39279000-39279800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:39279000-39283400	Weak transcription	HSMM	muscle
11	chr19:39279200-39279800	Enhancers	Fetal Muscle Trunk	muscle
12	chr19:39279200-39279800	Enhancers	Stomach Mucosa	stomach
13	chr19:39279400-39279800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr19:39279400-39279800	Enhancers	Fetal Muscle Leg	muscle
15	chr19:39279400-39283400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr19:39279600-39279800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr19:39279600-39279800	Enhancers	HMEC	breast
18	chr19:39279600-39279800	Active TSS	NHEK	skin
19	chr19:39279600-39280800	Weak transcription	Esophagus	oesophagus
20	chr19:39279600-39281400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr19:39279600-39281800	Weak transcription	Fetal Intestine Large	intestine
22	chr19:39279600-39281800	Weak transcription	Fetal Intestine Small	intestine
23	chr19:39279600-39281800	Weak transcription	Fetal Thymus	thymus
24	chr19:39279600-39282800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr19:39279600-39282800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr19:39279600-39283000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:39279600-39283000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr19:39279600-39283200	Weak transcription	HepG2	liver
29	chr19:39279600-39283400	Weak transcription	A549	lung

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