Variant report

Variant	rs8177184
Chromosome Location	chr3:133464496-133464497
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR3C1	chr3:133464309-133464596	A549	lung:	n/a	chr3:133464493-133464507 chr3:133464443-133464469 chr3:133464487-133464513 chr3:133464487-133464513 chr3:133464487-133464513 chr3:133464424-133464440 chr3:133464487-133464513 chr3:133464446-133464455
2	MAFK	chr3:133464074-133464731	HepG2	liver:	n/a	n/a
3	MYBL2	chr3:133464363-133465626	HepG2	liver:	n/a	n/a
4	MYBL2	chr3:133464479-133466127	HepG2	liver:	n/a	n/a
5	NR3C1	chr3:133464344-133464598	A549	lung:	n/a	chr3:133464493-133464507 chr3:133464443-133464469 chr3:133464487-133464513 chr3:133464487-133464513 chr3:133464487-133464513 chr3:133464424-133464440 chr3:133464487-133464513 chr3:133464446-133464455
6	POLR2A	chr3:133464423-133479250	HepG2	liver:	n/a	n/a
7	MAFK	chr3:133464099-133465339	HepG2	liver:	n/a	n/a
8	HEY1	chr3:133464270-133467811	HepG2	liver:	n/a	chr3:133465389-133465404
9	POLR2A	chr3:133464411-133467827	HepG2	liver:	n/a	n/a
10	RAD21	chr3:133464419-133465474	HepG2	liver:	n/a	chr3:133464712-133464731 chr3:133464721-133464730
11	NR3C1	chr3:133464354-133464631	A549	lung:	n/a	chr3:133464493-133464507 chr3:133464443-133464469 chr3:133464487-133464513 chr3:133464487-133464513 chr3:133464487-133464513 chr3:133464424-133464440 chr3:133464487-133464513 chr3:133464446-133464455

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:133464463-133464513	SK-N-SH_RA	brain:	n/a
2	chr3:133464463-133464513	PFSK-1	brain:	n/a
3	chr3:133464463-133464513	HPAEpiC	pulmonary alveolar:	n/a
4	chr3:133464463-133464513	AoSMC	blood vessel:	n/a
5	chr3:133464463-133464513	GM12891	blood:	n/a
6	chr3:133464463-133464513	SK-N-SH	brain:	n/a
7	chr3:133464463-133464513	HRPEpiC	eye:	n/a
8	chr3:133464463-133464513	BJ	skin:	n/a
9	chr3:133464463-133464513	HRCEpiC	kidney:	n/a
10	chr3:133464463-133464513	NHDF-neo	bronchial:	n/a
11	chr3:133464463-133464513	RPTEC	kidney:	n/a
12	chr3:133464463-133464513	LNCaP	prostate:	n/a
13	chr3:133464463-133464513	H1-hESC	embryonic stem cell:	embryo
14	chr3:133464463-133464513	NHBE	bronchial:	n/a
15	chr3:133464463-133464513	HNPCEpiC	eye:	n/a
16	chr3:133464463-133464513	A549	lung:	n/a
17	chr3:133464463-133464513	Caco-2	colon:	n/a
18	chr3:133464463-133464513	HRE	kidney:	n/a
19	chr3:133464463-133464513	HCPEpiC	choroid plexus:	n/a
20	chr3:133464463-133464513	AG04450	lung:	fetal
21	chr3:133464463-133464513	HMEC	breast:	n/a
22	chr3:133464463-133464513	GM19239	blood:	n/a
23	chr3:133464463-133464513	U87	brain:	n/a
24	chr3:133464463-133464513	Hepatocyte	liver:	n/a
25	chr3:133464463-133464513	AG10803	skin:	n/a
26	chr3:133464463-133464513	GM12892	blood:	n/a
27	chr3:133464463-133464513	K562	blood:	n/a
28	chr3:133464463-133464513	Jurkat	blood:	n/a
29	chr3:133464463-133464513	AG09319	gingival:	n/a
30	chr3:133464463-133464513	GM06990	blood:	n/a
31	chr3:133464463-133464513	SKMC	muscle:	n/a
32	chr3:133464463-133464513	HIPEpiC	eye:	n/a
33	chr3:133464463-133464513	BE2_C	brain:	n/a
34	chr3:133464463-133464513	NH-A	brain:	n/a
35	chr3:133464463-133464513	ECC-1	luminal epithelium:	n/a
36	chr3:133464463-133464513	PrEC	prostate:	n/a
37	chr3:133464463-133464513	AG04449	skin:	fetal
38	chr3:133464463-133464513	PANC-1	pancreas:	n/a
39	chr3:133464463-133464513	HL-60	blood:	n/a
40	chr3:133464463-133464513	T-47D	breast:	n/a
41	chr3:133464463-133464513	HEK293	kidney:	embryo
42	chr3:133464463-133464513	SK-N-MC	brain:	n/a
43	chr3:133464463-133464513	HepG2	liver:	n/a
44	chr3:133464463-133464513	HAEpiC	amniotic membrane:	n/a
45	chr3:133464463-133464513	MCF10A-Er-Src	breast:	n/a
46	chr3:133464463-133464513	MCF-7	breast:	n/a
47	chr3:133464463-133464513	Hela-S3	cervix:	n/a
48	chr3:133464463-133464513	HCF	heart:	n/a
49	chr3:133464463-133464513	HEEpiC	esophagus:	n/a
50	chr3:133464463-133464513	HCT-116	colon:	n/a

Variant related genes	Relation type
TF	TF binding region
TF	CpG island

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10049093	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10935081	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10935083	0.91[ASN][1000 genomes]
rs11715340	0.87[ASN][1000 genomes]
rs11717407	0.88[ASN][1000 genomes]
rs16840692	0.84[ASN][1000 genomes]
rs16840699	0.88[ASN][1000 genomes]
rs16840751	0.89[ASN][1000 genomes]
rs16840812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1799852	0.82[JPT][hapmap]
rs4241356	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4428180	1.00[ASW][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4532136	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4582061	0.88[ASN][1000 genomes]
rs4854595	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4854748	0.97[ASN][1000 genomes]
rs4854749	0.97[ASN][1000 genomes]
rs4854750	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4854752	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4854754	0.89[ASN][1000 genomes]
rs4854755	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4854757	0.91[ASN][1000 genomes]
rs6801244	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8177181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8177185	0.92[CHD][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.93[MKK][hapmap];0.91[ASN][1000 genomes]
rs8177186	0.92[CHD][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.93[MKK][hapmap];0.91[ASN][1000 genomes]
rs8177203	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs8177215	0.82[JPT][hapmap]
rs9714237	0.84[ASN][1000 genomes]
rs9847885	0.88[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	nsv877506	chr3:133423473-133569777	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer 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	10 gene(s)	inside rSNPs	diseases
2	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised 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	12 gene(s)	inside rSNPs	diseases
3	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8177184	NCK1	cis	cerebellum	SCAN
rs8177184	EPB42	trans	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133460400-133464600	Enhancers	Brain Inferior Temporal Lobe	brain
2	chr3:133460800-133464600	Enhancers	Brain Angular Gyrus	brain
3	chr3:133461800-133464600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:133462000-133464600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:133463400-133465200	Flanking Active TSS	Liver	Liver
6	chr3:133463600-133465200	Weak transcription	Spleen	Spleen
7	chr3:133464200-133464600	Flanking Active TSS	HepG2	liver
8	chr3:133464400-133464600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
9	chr3:133464400-133464600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:133464400-133464600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr3:133464400-133464600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:133464400-133464600	Active TSS	Brain Anterior Caudate	brain
13	chr3:133464400-133464600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:133464400-133464600	Bivalent Enhancer	Fetal Brain Female	brain
15	chr3:133464400-133464800	Bivalent Enhancer	Adipose Nuclei	Adipose
16	chr3:133464400-133464800	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr3:133464400-133464800	Flanking Active TSS	Brain Hippocampus Middle	brain
18	chr3:133464400-133464800	Flanking Active TSS	Brain Substantia Nigra	brain
19	chr3:133464400-133465800	Enhancers	Pancreas	Pancrea
20	chr3:133464400-133466400	Weak transcription	K562	blood

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