Variant report

Variant	rs28548813
Chromosome Location	chr15:31192896-31192897
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: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	chr15:31192891-31192941	BJ	skin:	n/a
2	chr15:31192891-31192941	HCPEpiC	choroid plexus:	n/a
3	chr15:31192891-31192941	HUVEC	blood vessel:	n/a
4	chr15:31192891-31192941	AoSMC	blood vessel:	n/a
5	chr15:31192891-31192941	NB4	blood:	n/a
6	chr15:31192891-31192941	GM06990	blood:	n/a
7	chr15:31192891-31192941	GM12878	blood:	n/a
8	chr15:31192891-31192941	BE2_C	brain:	n/a
9	chr15:31192891-31192941	AG09319	gingival:	n/a
10	chr15:31192891-31192941	PrEC	prostate:	n/a
11	chr15:31192891-31192941	ECC-1	luminal epithelium:	n/a
12	chr15:31192891-31192941	HPAEpiC	pulmonary alveolar:	n/a
13	chr15:31192891-31192941	HEEpiC	esophagus:	n/a
14	chr15:31192891-31192941	MCF-7	breast:	n/a
15	chr15:31192891-31192941	Hepatocyte	liver:	n/a
16	chr15:31192891-31192941	HCT-116	colon:	n/a
17	chr15:31192891-31192941	SAEC	small airway:	n/a
18	chr15:31192891-31192941	IMR90	lung:	fetal
19	chr15:31192891-31192941	ovcar-3	ovarian:	n/a
20	chr15:31192891-31192941	ProgFib	skin:	n/a
21	chr15:31192891-31192941	HL-60	blood:	n/a
22	chr15:31192891-31192941	HCM	heart:	n/a
23	chr15:31192891-31192941	NT2-D1	testis:	n/a
24	chr15:31192891-31192941	SK-N-SH	brain:	n/a
25	chr15:31192891-31192941	PANC-1	pancreas:	n/a
26	chr15:31192891-31192941	GM12892	blood:	n/a
27	chr15:31192891-31192941	MCF10A-Er-Src	breast:	n/a
28	chr15:31192891-31192941	HIPEpiC	eye:	n/a
29	chr15:31192891-31192941	HMEC	breast:	n/a
30	chr15:31192891-31192941	HepG2	liver:	n/a
31	chr15:31192891-31192941	Caco-2	colon:	n/a
32	chr15:31192891-31192941	NHBE	bronchial:	n/a
33	chr15:31192891-31192941	SKMC	muscle:	n/a
34	chr15:31192891-31192941	T-47D	breast:	n/a
35	chr15:31192891-31192941	HRCEpiC	kidney:	n/a
36	chr15:31192891-31192941	Hela-S3	cervix:	n/a
37	chr15:31192891-31192941	AG10803	skin:	n/a
38	chr15:31192891-31192941	K562	blood:	n/a
39	chr15:31192891-31192941	HCF	heart:	n/a
40	chr15:31192891-31192941	AG04450	lung:	fetal
41	chr15:31192891-31192941	HAEpiC	amniotic membrane:	n/a
42	chr15:31192891-31192941	A549	lung:	n/a
43	chr15:31192891-31192941	AG04449	skin:	fetal
44	chr15:31192891-31192941	RPTEC	kidney:	n/a
45	chr15:31192891-31192941	HRE	kidney:	n/a
46	chr15:31192891-31192941	U87	brain:	n/a
47	chr15:31192891-31192941	HRPEpiC	eye:	n/a
48	chr15:31192891-31192941	NH-A	brain:	n/a
49	chr15:31192891-31192941	PFSK-1	brain:	n/a
50	chr15:31192891-31192941	H1-hESC	embryonic stem cell:	embryo

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAN1-3	chr15:31192343-31193819	NONHSAT041414

No data

Variant related genes	Relation type
FAN1	CpG island

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10163148	0.80[ASN][1000 genomes]
rs11070624	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11631543	1.00[ASN][1000 genomes]
rs11856544	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12441318	1.00[ASN][1000 genomes]
rs12907055	0.80[ASN][1000 genomes]
rs1474382	0.80[ASN][1000 genomes]
rs1524878	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1852034	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1880500	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177669	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2293314	1.00[ASN][1000 genomes]
rs2339043	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28693590	0.80[ASN][1000 genomes]
rs28708881	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28721380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28795529	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2949566	1.00[ASN][1000 genomes]
rs2955794	0.83[ASN][1000 genomes]
rs2955796	1.00[ASN][1000 genomes]
rs2955798	1.00[ASN][1000 genomes]
rs2959039	1.00[ASN][1000 genomes]
rs35162264	0.80[ASN][1000 genomes]
rs3829484	0.81[ASN][1000 genomes]
rs4779796	0.80[ASN][1000 genomes]
rs4779797	0.80[ASN][1000 genomes]
rs56325201	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58844471	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7169064	0.80[ASN][1000 genomes]
rs739831	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8023264	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9806159	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427955	chr15:30467980-31273174	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv916936	chr15:30921917-31337510	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv525795	chr15:30936285-31324531	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv533434	chr15:30938215-31244225	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
7	nsv1046874	chr15:31008133-31294654	Enhancers Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
9	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
10	nsv832951	chr15:31131239-31304469	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv1039037	chr15:31140415-31277268	Strong transcription ZNF genes & repeats Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv542309	chr15:31140415-31277268	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
13	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
14	nsv521842	chr15:31140700-31272670	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
15	nsv903834	chr15:31179534-31293774	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	esv33507	chr15:31183324-31471023	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
17	nsv974549	chr15:31183683-31193060	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28548813	RP11-540B6.2	cis	Whole Blood	GTEx
rs28548813	RP11-540B6.3	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31132800-31195600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:31187000-31195400	Weak transcription	NH-A	brain
3	chr15:31187000-31195600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:31188400-31193000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:31192600-31195000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr15:31192800-31194200	Strong transcription	Dnd41	blood

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