Variant report

Variant	rs5082
Chromosome Location	chr1:161193683-161193684
allele	C/T
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	POLR2A	chr1:161187638-161194598	HepG2	liver:	n/a	n/a
2	RCOR1	chr1:161193071-161194387	HepG2	liver:	n/a	n/a
3	EP300	chr1:161193122-161194526	HepG2	liver:	n/a	n/a
4	EP300	chr1:161193077-161194620	HepG2	liver:	n/a	n/a
5	RFX5	chr1:161193327-161194384	HepG2	liver:	n/a	n/a
6	NFIC	chr1:161192770-161194564	HepG2	liver:	n/a	n/a
7	ELF1	chr1:161193165-161193692	HepG2	liver:	n/a	n/a
8	MYBL2	chr1:161191656-161194634	HepG2	liver:	n/a	n/a
9	FOXA2	chr1:161193055-161194460	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:161191743-161194547	HepG2	liver:	n/a	n/a
11	SP1	chr1:161192940-161194595	HepG2	liver:	n/a	chr1:161194261-161194270 chr1:161194255-161194265 chr1:161194257-161194271 chr1:161194255-161194264 chr1:161193502-161193511 chr1:161194251-161194265 chr1:161193583-161193597
12	RXRA	chr1:161193211-161194537	HepG2	liver:	n/a	n/a
13	FOXA1	chr1:161193132-161194538	HepG2	liver:	n/a	n/a
14	NFIC	chr1:161192817-161194565	HepG2	liver:	n/a	n/a
15	MXI1	chr1:161193208-161194390	HepG2	liver:	n/a	n/a
16	TCF7L2	chr1:161193504-161194475	HepG2	liver:	n/a	n/a
17	HEY1	chr1:161191669-161194540	HepG2	liver:	n/a	n/a
18	REST	chr1:161192938-161194617	HepG2	liver:	n/a	n/a
19	SMC3	chr1:161193246-161194409	HepG2	liver:	n/a	n/a
20	CEBPD	chr1:161193036-161193688	HepG2	liver:	n/a	n/a
21	ARID3A	chr1:161193290-161194493	HepG2	liver:	n/a	n/a
22	EP300	chr1:161193267-161194467	HepG2	liver:	n/a	n/a
23	NR2F2	chr1:161193020-161194629	HepG2	liver:	n/a	n/a
24	POLR2A	chr1:161187501-161194535	HepG2	liver:	n/a	n/a
25	RXRA	chr1:161193157-161194536	HepG2	liver:	n/a	n/a
26	POLR2A	chr1:161187261-161194848	HepG2	liver:	n/a	n/a
27	POLR2A	chr1:161193176-161194096	HepG2	liver:	n/a	n/a
28	MBD4	chr1:161191635-161194538	HepG2	liver:	n/a	n/a
29	FOXA1	chr1:161193072-161193713	HepG2	liver:	n/a	n/a
30	HEY1	chr1:161187602-161194631	HepG2	liver:	n/a	n/a
31	TBP	chr1:161193190-161194483	HepG2	liver:	n/a	n/a
32	MYBL2	chr1:161192315-161194692	HepG2	liver:	n/a	n/a
33	POLR2A	chr1:161192579-161194236	HepG2	liver:	n/a	n/a
34	RAD21	chr1:161193324-161194437	HepG2	liver:	n/a	n/a
35	POLR2A	chr1:161192676-161194507	HepG2	liver:	n/a	n/a
36	MAX	chr1:161193224-161193818	HepG2	liver:	n/a	chr1:161193559-161193575 chr1:161193588-161193598
37	NR2F2	chr1:161191611-161194624	HepG2	liver:	n/a	n/a
38	MBD4	chr1:161191636-161194471	HepG2	liver:	n/a	n/a
39	MYC	chr1:161193210-161193746	HepG2	liver:	n/a	chr1:161193559-161193575 chr1:161193588-161193598
40	BHLHE40	chr1:161193143-161194415	HepG2	liver:	n/a	n/a
41	FOSL2	chr1:161193037-161193722	HepG2	liver:	n/a	n/a
42	POLR2A	chr1:161191482-161194479	HepG2	liver:	n/a	n/a
43	MAZ	chr1:161193188-161194459	HepG2	liver:	n/a	chr1:161193559-161193575 chr1:161193588-161193598
44	FOXA2	chr1:161193170-161193727	HepG2	liver:	n/a	n/a
45	TEAD4	chr1:161192958-161194688	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:161191256..161193783-chr1:161281655..161284632,2	K562	blood:
2	chr1:161191860..161194631-chr1:161195444..161197295,2	MCF-7	breast:
3	chr1:161192625..161198260-chr1:161274899..161278564,8	K562	blood:
4	chr1:161144654..161146766-chr1:161192298..161194395,2	MCF-7	breast:
5	chr1:161192147..161195116-chr1:161197570..161199818,2	MCF-7	breast:
6	chr1:161173950..161176366-chr1:161191214..161193773,2	MCF-7	breast:

Variant related genes	Relation type
APOA2	TF binding region
TOMM40L	TF binding region
MIR5187	TF binding region
ENSG00000158850	Chromatin interaction
ENSG00000158864	Chromatin interaction
ENSG00000158887	Chromatin interaction
ENSG00000263548	Chromatin interaction
ENSG00000158882	Chromatin interaction
ENSG00000143252	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10797094	0.81[GIH][hapmap]
rs2502802	0.85[YRI][hapmap]
rs4073054	0.84[ASW][hapmap];0.96[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4589131	0.81[GIH][hapmap]
rs4634925	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4656292	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4656993	0.80[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs5082	OR6N2	cis	parietal	SCAN
rs5082	FCRL2	cis	parietal	SCAN
rs5082	PVRL4	cis	parietal	SCAN
rs5082	B4GALT3	cis	cerebellum	SCAN
rs5082	OR10J5	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161182400-161193800	Weak transcription	Small Intestine	intestine
2	chr1:161184400-161195000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:161184400-161195000	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:161184400-161195000	Weak transcription	NHEK	skin
5	chr1:161184600-161195000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:161184600-161195000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:161184600-161195000	Weak transcription	Brain Substantia Nigra	brain
8	chr1:161184600-161195800	Weak transcription	Aorta	Aorta
9	chr1:161184600-161195800	Weak transcription	Esophagus	oesophagus
10	chr1:161185000-161194800	Weak transcription	Dnd41	blood
11	chr1:161185000-161195000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:161185200-161195000	Weak transcription	A549	lung
13	chr1:161185200-161195200	Weak transcription	Thymus	Thymus
14	chr1:161185400-161195200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:161185400-161195200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:161185400-161195200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:161185600-161195000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:161185600-161195200	Weak transcription	HMEC	breast
19	chr1:161185800-161195000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:161185800-161195800	Enhancers	Fetal Intestine Large	intestine
21	chr1:161186000-161194000	Weak transcription	Gastric	stomach
22	chr1:161186000-161195200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:161186600-161194000	Weak transcription	Stomach Mucosa	stomach
24	chr1:161186800-161194800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr1:161186800-161195000	Weak transcription	Brain Angular Gyrus	brain
26	chr1:161187000-161195000	Weak transcription	Fetal Lung	lung
27	chr1:161187400-161195800	Weak transcription	Lung	lung
28	chr1:161187600-161194200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:161187600-161195200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:161187800-161195000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:161187800-161195000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:161187800-161195000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr1:161188200-161195000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:161188200-161195000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:161188400-161195000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:161188400-161195000	Weak transcription	Adipose Nuclei	Adipose
37	chr1:161188600-161195000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:161189000-161195200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr1:161189600-161195000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:161189800-161195000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:161190000-161195000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr1:161190000-161195000	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:161190000-161195000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr1:161190000-161195200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr1:161190200-161194800	Weak transcription	Primary T cells from cord blood	blood
46	chr1:161190200-161195000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr1:161190200-161195000	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr1:161190800-161194000	Weak transcription	K562	blood
49	chr1:161190800-161194400	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr1:161190800-161195000	Weak transcription	Spleen	Spleen

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