Variant report

Variant	rs62120085
Chromosome Location	chr19:39235278-39235279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39235205-39235330	HepG2	liver:	n/a	n/a
2	BCL3	chr19:39234810-39235328	A549	lung:	n/a	n/a
3	POLR2A	chr19:39234412-39235375	K562	blood:	n/a	n/a
4	POLR2A	chr19:39233308-39235337	PANC-1	pancreas:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:39235278-39235328	HEEpiC	esophagus:	n/a
2	chr19:39235278-39235328	AoSMC	blood vessel:	n/a
3	chr19:39235278-39235328	K562	blood:	n/a
4	chr19:39235278-39235328	GM12891	blood:	n/a
5	chr19:39235278-39235328	MCF-7	breast:	n/a
6	chr19:39235278-39235328	HCM	heart:	n/a
7	chr19:39235278-39235328	HUVEC	blood vessel:	n/a
8	chr19:39235278-39235328	Jurkat	blood:	n/a
9	chr19:39235278-39235328	HEK293	kidney:	embryo
10	chr19:39235278-39235328	HepG2	liver:	n/a
11	chr19:39235278-39235328	HCF	heart:	n/a
12	chr19:39235278-39235328	MCF10A-Er-Src	breast:	n/a
13	chr19:39235278-39235328	GM12892	blood:	n/a
14	chr19:39235278-39235328	PFSK-1	brain:	n/a
15	chr19:39235278-39235328	HIPEpiC	eye:	n/a
16	chr19:39235278-39235328	BE2_C	brain:	n/a
17	chr19:39235278-39235328	SAEC	small airway:	n/a
18	chr19:39235278-39235328	HPAEpiC	pulmonary alveolar:	n/a
19	chr19:39235278-39235328	NHDF-neo	bronchial:	n/a
20	chr19:39235278-39235328	ProgFib	skin:	n/a
21	chr19:39235278-39235328	BJ	skin:	n/a
22	chr19:39235278-39235328	HRCEpiC	kidney:	n/a
23	chr19:39235278-39235328	AG09319	gingival:	n/a
24	chr19:39235278-39235328	HRE	kidney:	n/a
25	chr19:39235278-39235328	HAEpiC	amniotic membrane:	n/a
26	chr19:39235278-39235328	GM12878	blood:	n/a
27	chr19:39235278-39235328	RPTEC	kidney:	n/a
28	chr19:39235278-39235328	Caco-2	colon:	n/a
29	chr19:39235278-39235328	U87	brain:	n/a
30	chr19:39235278-39235328	ECC-1	luminal epithelium:	n/a
31	chr19:39235278-39235328	GM19239	blood:	n/a
32	chr19:39235278-39235328	SK-N-MC	brain:	n/a
33	chr19:39235278-39235328	HCPEpiC	choroid plexus:	n/a
34	chr19:39235278-39235328	AG04449	skin:	fetal
35	chr19:39235278-39235328	SKMC	muscle:	n/a
36	chr19:39235278-39235328	AG04450	lung:	fetal
37	chr19:39235278-39235328	A549	lung:	n/a
38	chr19:39235278-39235328	CMK	blood:	n/a
39	chr19:39235278-39235328	NHBE	bronchial:	n/a
40	chr19:39235278-39235328	GM06990	blood:	n/a
41	chr19:39235278-39235328	PrEC	prostate:	n/a
42	chr19:39235278-39235328	AG09309	skin:	n/a
43	chr19:39235278-39235328	Hepatocyte	liver:	n/a
44	chr19:39235278-39235328	NB4	blood:	n/a
45	chr19:39235278-39235328	HNPCEpiC	eye:	n/a
46	chr19:39235278-39235328	LNCaP	prostate:	n/a
47	chr19:39235278-39235328	HRPEpiC	eye:	n/a
48	chr19:39235278-39235328	HMEC	breast:	n/a
49	chr19:39235278-39235328	ovcar-3	ovarian:	n/a
50	chr19:39235278-39235328	IMR90	lung:	fetal

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39227687..39231006-chr19:39233180..39235814,6	K562	blood:
2	chr19:39227434..39229644-chr19:39233125..39236145,3	MCF-7	breast:
3	chr19:39228662..39230704-chr19:39233193..39235780,3	K562	blood:
4	chr19:39233778..39236095-chr19:39340274..39342606,2	K562	blood:

No data

Variant related genes	Relation type
CAPN12	TF binding region
CAPN12	CpG island
ENSG00000182472	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000267892	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1106372	0.89[ASN][1000 genomes]
rs12972987	0.89[ASN][1000 genomes]
rs12977631	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12978273	0.89[ASN][1000 genomes]
rs12979149	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12980798	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12983550	0.89[ASN][1000 genomes]
rs12985871	0.89[ASN][1000 genomes]
rs12986032	0.89[ASN][1000 genomes]
rs2001856	0.92[ASN][1000 genomes]
rs2368524	0.84[AMR][1000 genomes]
rs34090445	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34911882	0.89[ASN][1000 genomes]
rs35007285	0.89[ASN][1000 genomes]
rs35096737	0.92[ASN][1000 genomes]
rs35403788	0.89[ASN][1000 genomes]
rs35855940	0.92[ASN][1000 genomes]
rs4491650	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4802774	0.81[ASN][1000 genomes]
rs62120091	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62120094	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62121364	0.82[AMR][1000 genomes]
rs62121365	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	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
3	nsv817834	chr19:39174332-39237950	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer 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	14 gene(s)	inside rSNPs	diseases
4	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
5	esv1826260	chr19:39178364-39248836	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62120085	EIF3K	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39233200-39236000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr19:39234200-39235400	Enhancers	Spleen	Spleen
3	chr19:39234400-39236000	Enhancers	K562	blood
4	chr19:39235000-39235600	Enhancers	Primary T cells fromperipheralblood	blood
5	chr19:39235200-39236000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:39235200-39244400	Weak transcription	HepG2	liver

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