Variant report

Variant	rs2708904
Chromosome Location	chr7:48023085-48023086
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:2)
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	chr7:48023062-48023112	NB4	blood:	n/a
2	chr7:48023062-48023112	SKMC	muscle:	n/a
3	chr7:48023062-48023112	BE2_C	brain:	n/a
4	chr7:48023062-48023112	BJ	skin:	n/a
5	chr7:48023062-48023112	GM12891	blood:	n/a
6	chr7:48023062-48023112	HRCEpiC	kidney:	n/a
7	chr7:48023062-48023112	HepG2	liver:	n/a
8	chr7:48023062-48023112	GM12878	blood:	n/a
9	chr7:48023062-48023112	ProgFib	skin:	n/a
10	chr7:48023062-48023112	GM19239	blood:	n/a
11	chr7:48023062-48023112	PFSK-1	brain:	n/a
12	chr7:48023062-48023112	PANC-1	pancreas:	n/a
13	chr7:48023062-48023112	MCF-7	breast:	n/a
14	chr7:48023062-48023112	Caco-2	colon:	n/a
15	chr7:48023062-48023112	HRPEpiC	eye:	n/a
16	chr7:48023062-48023112	AG04450	lung:	fetal
17	chr7:48023062-48023112	HAEpiC	amniotic membrane:	n/a
18	chr7:48023062-48023112	T-47D	breast:	n/a
19	chr7:48023062-48023112	AG09319	gingival:	n/a
20	chr7:48023062-48023112	RPTEC	kidney:	n/a
21	chr7:48023062-48023112	PrEC	prostate:	n/a
22	chr7:48023062-48023112	NHBE	bronchial:	n/a
23	chr7:48023062-48023112	GM12892	blood:	n/a
24	chr7:48023062-48023112	HCF	heart:	n/a
25	chr7:48023062-48023112	HCPEpiC	choroid plexus:	n/a
26	chr7:48023062-48023112	SAEC	small airway:	n/a
27	chr7:48023062-48023112	Jurkat	blood:	n/a
28	chr7:48023062-48023112	HEEpiC	esophagus:	n/a
29	chr7:48023062-48023112	AG04449	skin:	fetal
30	chr7:48023062-48023112	HRE	kidney:	n/a
31	chr7:48023062-48023112	HL-60	blood:	n/a
32	chr7:48023062-48023112	NH-A	brain:	n/a
33	chr7:48023062-48023112	K562	blood:	n/a
34	chr7:48023062-48023112	Hepatocyte	liver:	n/a
35	chr7:48023062-48023112	HCT-116	colon:	n/a
36	chr7:48023062-48023112	SK-N-SH_RA	brain:	n/a
37	chr7:48023062-48023112	AG10803	skin:	n/a
38	chr7:48023062-48023112	GM06990	blood:	n/a
39	chr7:48023062-48023112	NHDF-neo	bronchial:	n/a
40	chr7:48023062-48023112	HMEC	breast:	n/a
41	chr7:48023062-48023112	HIPEpiC	eye:	n/a
42	chr7:48023062-48023112	HCM	heart:	n/a
43	chr7:48023062-48023112	ovcar-3	ovarian:	n/a
44	chr7:48023062-48023112	HEK293	kidney:	embryo
45	chr7:48023062-48023112	Hela-S3	cervix:	n/a
46	chr7:48023062-48023112	HNPCEpiC	eye:	n/a
47	chr7:48023062-48023112	ECC-1	luminal epithelium:	n/a
48	chr7:48023062-48023112	AoSMC	blood vessel:	n/a
49	chr7:48023062-48023112	H1-hESC	embryonic stem cell:	embryo
50	chr7:48023062-48023112	A549	lung:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:48018249..48020588-chr7:48022807..48026428,3	K562	blood:
2	chr7:48019088..48020629-chr7:48022304..48024307,2	K562	blood:

No data

Variant related genes	Relation type
HUS1	CpG island
ENSG00000136273	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11763527	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2686844	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686845	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708906	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708908	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28880325	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3736546	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers 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	19 gene(s)	inside rSNPs	diseases
3	nsv830991	chr7:47854530-48025996	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2708904	UPP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48019400-48028800	Weak transcription	Fetal Lung	lung
2	chr7:48019800-48028200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:48019800-48031600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:48020800-48023600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr7:48022000-48023200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links