Variant report

Variant	rs9855348
Chromosome Location	chr3:112876738-112876739
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:1)
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	chr3:112876728-112876778	HCPEpiC	choroid plexus:	n/a
2	chr3:112876728-112876778	AG10803	skin:	n/a
3	chr3:112876728-112876778	T-47D	breast:	n/a
4	chr3:112876728-112876778	GM12891	blood:	n/a
5	chr3:112876728-112876778	ECC-1	luminal epithelium:	n/a
6	chr3:112876728-112876778	AG09319	gingival:	n/a
7	chr3:112876728-112876778	HL-60	blood:	n/a
8	chr3:112876728-112876778	PFSK-1	brain:	n/a
9	chr3:112876728-112876778	HepG2	liver:	n/a
10	chr3:112876728-112876778	HRE	kidney:	n/a
11	chr3:112876728-112876778	BE2_C	brain:	n/a
12	chr3:112876728-112876778	HRCEpiC	kidney:	n/a
13	chr3:112876728-112876778	AG04449	skin:	fetal
14	chr3:112876728-112876778	HUVEC	blood vessel:	n/a
15	chr3:112876728-112876778	HNPCEpiC	eye:	n/a
16	chr3:112876728-112876778	HCF	heart:	n/a
17	chr3:112876728-112876778	ProgFib	skin:	n/a
18	chr3:112876728-112876778	HCM	heart:	n/a
19	chr3:112876728-112876778	IMR90	lung:	fetal
20	chr3:112876728-112876778	H1-hESC	embryonic stem cell:	embryo
21	chr3:112876728-112876778	HRPEpiC	eye:	n/a
22	chr3:112876728-112876778	AG04450	lung:	fetal
23	chr3:112876728-112876778	PANC-1	pancreas:	n/a
24	chr3:112876728-112876778	NB4	blood:	n/a
25	chr3:112876728-112876778	RPTEC	kidney:	n/a
26	chr3:112876728-112876778	MCF-7	breast:	n/a
27	chr3:112876728-112876778	Caco-2	colon:	n/a
28	chr3:112876728-112876778	HEK293	kidney:	embryo
29	chr3:112876728-112876778	A549	lung:	n/a
30	chr3:112876728-112876778	NHDF-neo	bronchial:	n/a
31	chr3:112876728-112876778	BJ	skin:	n/a
32	chr3:112876728-112876778	LNCaP	prostate:	n/a
33	chr3:112876728-112876778	Hela-S3	cervix:	n/a
34	chr3:112876728-112876778	GM12892	blood:	n/a
35	chr3:112876728-112876778	MCF10A-Er-Src	breast:	n/a
36	chr3:112876728-112876778	PrEC	prostate:	n/a
37	chr3:112876728-112876778	K562	blood:	n/a
38	chr3:112876728-112876778	GM19239	blood:	n/a
39	chr3:112876728-112876778	GM12878	blood:	n/a
40	chr3:112876728-112876778	SK-N-MC	brain:	n/a
41	chr3:112876728-112876778	HIPEpiC	eye:	n/a
42	chr3:112876728-112876778	Hepatocyte	liver:	n/a
43	chr3:112876728-112876778	CMK	blood:	n/a
44	chr3:112876728-112876778	AoSMC	blood vessel:	n/a
45	chr3:112876728-112876778	NH-A	brain:	n/a
46	chr3:112876728-112876778	NHBE	bronchial:	n/a
47	chr3:112876728-112876778	HMEC	breast:	n/a
48	chr3:112876728-112876778	AG09309	skin:	n/a
49	chr3:112876728-112876778	HCT-116	colon:	n/a
50	chr3:112876728-112876778	NT2-D1	testis:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112875811..112877981-chr3:112929321..112930900,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GTPBP8-1	chr3:112876555-112876859	XLOC_002760

No data

Variant related genes	Relation type
ENSG00000240057	CpG island
ENSG00000144857	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10934222	0.85[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10934223	0.81[EUR][1000 genomes]
rs10934224	0.81[EUR][1000 genomes]
rs11712319	0.85[ASN][1000 genomes]
rs11716722	0.85[ASN][1000 genomes]
rs11720141	0.85[ASN][1000 genomes]
rs11923603	0.86[ASN][1000 genomes]
rs12490566	0.82[ASN][1000 genomes]
rs12631163	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12631199	0.85[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12634099	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2178398	0.85[ASN][1000 genomes]
rs2204788	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2204789	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2700229	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3732812	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4528911	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4555493	0.85[ASN][1000 genomes]
rs62262801	0.85[ASN][1000 genomes]
rs62264166	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62264172	0.81[EUR][1000 genomes]
rs6770160	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112871000-112881400	Weak transcription	Fetal Lung	lung
2	chr3:112874800-112877600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:112874800-112878000	Enhancers	Colon Smooth Muscle	Colon
4	chr3:112875600-112876800	Enhancers	Fetal Kidney	kidney
5	chr3:112875600-112880200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:112875800-112877600	Enhancers	Rectal Smooth Muscle	rectum
7	chr3:112875800-112878400	Enhancers	Fetal Stomach	stomach
8	chr3:112876000-112877000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:112876000-112877000	Enhancers	HSMMtube	muscle
10	chr3:112876000-112877200	Enhancers	Stomach Smooth Muscle	stomach
11	chr3:112876200-112876800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:112876200-112877000	Enhancers	Fetal Muscle Leg	muscle
13	chr3:112876400-112876800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:112876400-112877200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:112876600-112877000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:112876600-112877000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:112876600-112877600	Enhancers	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links