Variant report

Variant	rs2280327
Chromosome Location	chr4:165928581-165928582
allele	C/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:1)
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	chr4:165928549-165928599	HEK293	kidney:	embryo
2	chr4:165928549-165928599	AG04449	skin:	fetal
3	chr4:165928549-165928599	HMEC	breast:	n/a
4	chr4:165928549-165928599	AG09319	gingival:	n/a
5	chr4:165928549-165928599	CMK	blood:	n/a
6	chr4:165928549-165928599	AoSMC	blood vessel:	n/a
7	chr4:165928549-165928599	AG10803	skin:	n/a
8	chr4:165928549-165928599	MCF10A-Er-Src	breast:	n/a
9	chr4:165928549-165928599	AG09309	skin:	n/a
10	chr4:165928549-165928599	LNCaP	prostate:	n/a
11	chr4:165928549-165928599	Hepatocyte	liver:	n/a
12	chr4:165928549-165928599	AG04450	lung:	fetal
13	chr4:165928549-165928599	GM06990	blood:	n/a
14	chr4:165928549-165928599	NB4	blood:	n/a
15	chr4:165928549-165928599	MCF-7	breast:	n/a
16	chr4:165928549-165928599	T-47D	breast:	n/a
17	chr4:165928549-165928599	HRCEpiC	kidney:	n/a
18	chr4:165928549-165928599	IMR90	lung:	fetal
19	chr4:165928549-165928599	HRE	kidney:	n/a
20	chr4:165928549-165928599	HEEpiC	esophagus:	n/a
21	chr4:165928549-165928599	SAEC	small airway:	n/a
22	chr4:165928549-165928599	SK-N-MC	brain:	n/a
23	chr4:165928549-165928599	PANC-1	pancreas:	n/a
24	chr4:165928549-165928599	SK-N-SH_RA	brain:	n/a
25	chr4:165928549-165928599	Hela-S3	cervix:	n/a
26	chr4:165928549-165928599	BE2_C	brain:	n/a
27	chr4:165928549-165928599	H1-hESC	embryonic stem cell:	embryo
28	chr4:165928549-165928599	SK-N-SH	brain:	n/a
29	chr4:165928549-165928599	PrEC	prostate:	n/a
30	chr4:165928549-165928599	GM19239	blood:	n/a
31	chr4:165928549-165928599	U87	brain:	n/a
32	chr4:165928549-165928599	NT2-D1	testis:	n/a
33	chr4:165928549-165928599	Caco-2	colon:	n/a
34	chr4:165928549-165928599	HL-60	blood:	n/a
35	chr4:165928549-165928599	K562	blood:	n/a
36	chr4:165928549-165928599	HCT-116	colon:	n/a
37	chr4:165928549-165928599	HRPEpiC	eye:	n/a
38	chr4:165928549-165928599	ovcar-3	ovarian:	n/a
39	chr4:165928549-165928599	Jurkat	blood:	n/a
40	chr4:165928549-165928599	HPAEpiC	pulmonary alveolar:	n/a
41	chr4:165928549-165928599	NHDF-neo	bronchial:	n/a
42	chr4:165928549-165928599	NHBE	bronchial:	n/a
43	chr4:165928549-165928599	A549	lung:	n/a
44	chr4:165928549-165928599	GM12892	blood:	n/a
45	chr4:165928549-165928599	HAEpiC	amniotic membrane:	n/a
46	chr4:165928549-165928599	PFSK-1	brain:	n/a
47	chr4:165928549-165928599	BJ	skin:	n/a
48	chr4:165928549-165928599	NH-A	brain:	n/a
49	chr4:165928549-165928599	HCM	heart:	n/a
50	chr4:165928549-165928599	GM12878	blood:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM61-1	chr4:165928495-165929111	XLOC_004145

No data

Variant related genes	Relation type
ENSG00000250712	CpG island

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11942693	1.00[CEU][hapmap]
rs11942750	1.00[CEU][hapmap]
rs12510464	0.83[ASN][1000 genomes]
rs12647419	0.85[CEU][hapmap];0.98[EUR][1000 genomes]
rs12647427	0.87[CEU][hapmap];0.98[EUR][1000 genomes]
rs13111010	0.87[CEU][hapmap]
rs13137799	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13141887	0.91[EUR][1000 genomes]
rs13151735	0.81[CEU][hapmap];0.97[EUR][1000 genomes]
rs1401399	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1401400	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1401401	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2056252	0.91[EUR][1000 genomes]
rs2176634	0.98[EUR][1000 genomes]
rs2280325	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35449092	0.91[EUR][1000 genomes]
rs35680343	0.88[EUR][1000 genomes]
rs4690800	0.86[EUR][1000 genomes]
rs72697987	0.90[EUR][1000 genomes]
rs869867	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026152	chr4:165622244-166027447	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv537336	chr4:165622244-166027447	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking 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	36 gene(s)	inside rSNPs	diseases
3	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv880382	chr4:165793001-165964290	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	esv2757965	chr4:165801816-165976350	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv2759299	chr4:165801816-165976350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv528686	chr4:165814359-165930168	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv1015970	chr4:165852926-165973078	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv830140	chr4:165855999-165956612	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv533191	chr4:165879671-166171638	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:165925800-165929000	Weak transcription	Fetal Brain Male	brain
2	chr4:165927000-165930000	Weak transcription	Right Atrium	heart
3	chr4:165928000-165929000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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