Variant report

Variant	rs1885306
Chromosome Location	chr20:4795821-4795822
allele	A/C
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	MTA3	chr20:4793227-4796576	GM12878	blood:	n/a	n/a
2	POLR2A	chr20:4792105-4796734	GM12892	blood:	n/a	n/a
3	ELF1	chr20:4794729-4796598	GM12878	blood:	n/a	chr20:4794991-4795002
4	TBL1XR1	chr20:4793317-4796026	GM12878	blood:	n/a	n/a
5	ZEB1	chr20:4795502-4795872	GM12878	blood:	n/a	n/a
6	MAX	chr20:4795774-4795877	K562	blood:	n/a	chr20:4795832-4795841 chr20:4795832-4795841 chr20:4795830-4795843 chr20:4795832-4795841 chr20:4795830-4795843 chr20:4795830-4795843
7	USF2	chr20:4793875-4796111	GM12878	blood:	n/a	chr20:4795796-4795807 chr20:4793878-4793894 chr20:4795830-4795843 chr20:4795831-4795842 chr20:4795832-4795841 chr20:4795826-4795847 chr20:4795831-4795840 chr20:4795833-4795842 chr20:4795832-4795841
8	MTA3	chr20:4792292-4796722	GM12878	blood:	n/a	n/a
9	USF2	chr20:4795655-4795989	H1-hESC	embryonic stem cell:	n/a	chr20:4795796-4795807 chr20:4795830-4795843 chr20:4795831-4795842 chr20:4795832-4795841 chr20:4795826-4795847 chr20:4795831-4795840 chr20:4795833-4795842 chr20:4795832-4795841
10	POLR2A	chr20:4792201-4796647	GM12878	blood:	n/a	n/a
11	NFIC	chr20:4793640-4796642	GM12878	blood:	n/a	n/a
12	EP300	chr20:4793232-4795991	GM12878	blood:	n/a	chr20:4793902-4793916 chr20:4794992-4795001 chr20:4794998-4795008
13	ATF2	chr20:4793613-4796230	GM12878	blood:	n/a	n/a
14	CUX1	chr20:4794299-4796057	GM12878	blood:	n/a	n/a
15	USF1	chr20:4795714-4795926	HepG2	liver:	n/a	chr20:4795830-4795843 chr20:4795832-4795841 chr20:4795826-4795847 chr20:4795831-4795842 chr20:4795831-4795840 chr20:4795833-4795842 chr20:4795832-4795841 chr20:4795797-4795808
16	USF1	chr20:4795580-4795972	H1-hESC	embryonic stem cell:	n/a	chr20:4795830-4795843 chr20:4795832-4795841 chr20:4795826-4795847 chr20:4795831-4795842 chr20:4795831-4795840 chr20:4795833-4795842 chr20:4795832-4795841 chr20:4795797-4795808
17	RELA	chr20:4792744-4796241	GM18951	blood:	n/a	chr20:4795384-4795393 chr20:4795384-4795393 chr20:4795446-4795455 chr20:4795446-4795455
18	POLR2A	chr20:4793406-4796284	GM12878	blood:	n/a	n/a
19	NFATC1	chr20:4793734-4795956	GM12878	blood:	n/a	chr20:4795461-4795474
20	POLR2A	chr20:4792183-4796668	GM18526	blood:	n/a	n/a
21	STAT5A	chr20:4794621-4796111	GM12878	blood:	n/a	chr20:4795734-4795757
22	RELA	chr20:4793137-4795980	GM12878	blood:	n/a	chr20:4795384-4795393 chr20:4795384-4795393 chr20:4795446-4795455 chr20:4795446-4795455
23	POLR2A	chr20:4793264-4796189	GM12891	blood:	n/a	n/a
24	POLR2A	chr20:4792226-4796866	GM18951	blood:	n/a	n/a
25	POLR2A	chr20:4791978-4796555	GM15510	blood:	n/a	n/a
26	MAX	chr20:4793219-4796139	GM12878	blood:	n/a	chr20:4795832-4795841 chr20:4795832-4795841 chr20:4795830-4795843 chr20:4795573-4795583 chr20:4795832-4795841 chr20:4795830-4795843 chr20:4795573-4795583 chr20:4795830-4795843
27	PAX5	chr20:4794808-4795911	GM12878	blood:	n/a	chr20:4794991-4795000 chr20:4795259-4795268
28	EBF1	chr20:4794860-4795822	GM12878	blood:	n/a	chr20:4795061-4795070 chr20:4795061-4795071
29	POLR2A	chr20:4794713-4796050	GM12878	blood:	n/a	n/a
30	USF1	chr20:4795687-4795938	HepG2	liver:	n/a	chr20:4795830-4795843 chr20:4795832-4795841 chr20:4795826-4795847 chr20:4795831-4795842 chr20:4795831-4795840 chr20:4795833-4795842 chr20:4795832-4795841 chr20:4795797-4795808
31	MAZ	chr20:4793295-4796072	GM12878	blood:	n/a	chr20:4795832-4795841 chr20:4795832-4795841 chr20:4795830-4795843 chr20:4795573-4795583 chr20:4795832-4795841 chr20:4795830-4795843 chr20:4795573-4795583 chr20:4795830-4795843
32	SPI1	chr20:4794773-4795882	GM12878	blood:	n/a	chr20:4795555-4795568 chr20:4794992-4795001 chr20:4794990-4795003 chr20:4795050-4795063 chr20:4794991-4795004
33	PAX5	chr20:4795200-4795901	GM12878	blood:	n/a	chr20:4795259-4795268
34	POLR2A	chr20:4793073-4796580	GM12878	blood:	n/a	n/a
35	PML	chr20:4794784-4795840	GM12878	blood:	n/a	n/a
36	RELA	chr20:4793082-4796487	GM10847	blood:	n/a	chr20:4795384-4795393 chr20:4795384-4795393 chr20:4795446-4795455 chr20:4795446-4795455
37	BHLHE40	chr20:4793721-4796624	GM12878	blood:	n/a	chr20:4793878-4793894 chr20:4795830-4795843 chr20:4795832-4795841 chr20:4795826-4795847 chr20:4793872-4793888 chr20:4795831-4795840 chr20:4795833-4795842 chr20:4795832-4795841
38	EBF1	chr20:4794919-4796105	GM12878	blood:	n/a	chr20:4795061-4795070 chr20:4795061-4795071
39	POLR2A	chr20:4792210-4796639	GM12892	blood:	n/a	n/a
40	POU2F2	chr20:4794749-4795823	GM12878	blood:	n/a	n/a
41	TBP	chr20:4793222-4796557	GM12878	blood:	n/a	chr20:4793501-4793512
42	POLR2A	chr20:4793274-4796602	GM12878	blood:	n/a	n/a
43	STAT1	chr20:4793985-4796028	GM12878	blood:	n/a	chr20:4795734-4795757 chr20:4793993-4794005
44	YY1	chr20:4794771-4796057	GM12878	blood:	n/a	chr20:4795918-4795937
45	CHD1	chr20:4793704-4796133	GM12878	blood:	n/a	n/a
46	CEBPB	chr20:4793673-4796033	GM12878	blood:	n/a	n/a
47	RUNX3	chr20:4793109-4796627	GM12878	blood:	n/a	n/a
48	POLR2A	chr20:4793285-4796580	Raji	blood:	n/a	n/a
49	ZEB1	chr20:4795304-4796142	GM12878	blood:	n/a	n/a
50	EBF1	chr20:4792310-4796769	GM12878	blood:	n/a	chr20:4795061-4795070 chr20:4795061-4795071

Variant related genes	Relation type
RASSF2	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs13045004	0.81[EUR][1000 genomes]
rs1885308	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs2326550	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7271897	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs747748	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3373329	chr20:4082756-5007606	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530448	chr20:4575637-5030917	Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv912628	chr20:4751487-4836440	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv912629	chr20:4751487-5183353	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1885306	RASSF2	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:4778800-4796200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr20:4779200-4797400	Weak transcription	A549	lung
3	chr20:4779200-4802800	Weak transcription	Aorta	Aorta
4	chr20:4782000-4801600	Weak transcription	Fetal Intestine Small	intestine
5	chr20:4783400-4800400	Weak transcription	Fetal Brain Male	brain
6	chr20:4787000-4796400	Weak transcription	Brain Germinal Matrix	brain
7	chr20:4789000-4801200	Weak transcription	Ovary	ovary
8	chr20:4789800-4796600	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr20:4789800-4796800	Genic enhancers	Fetal Muscle Leg	muscle
10	chr20:4790000-4797000	Enhancers	Lung	lung
11	chr20:4790200-4796600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr20:4790200-4796800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr20:4790400-4796000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr20:4790400-4801400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr20:4791200-4799000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr20:4791600-4796600	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr20:4791800-4796000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr20:4791800-4796200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr20:4791800-4796200	Enhancers	Spleen	Spleen
20	chr20:4792000-4796200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr20:4792000-4796400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr20:4792200-4796600	Flanking Active TSS	GM12878-XiMat	blood
23	chr20:4792400-4796200	Flanking Active TSS	Primary B cells from peripheral blood	blood
24	chr20:4792400-4796200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr20:4792400-4796200	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr20:4792400-4796400	Enhancers	HUVEC	blood vessel
27	chr20:4792400-4796600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr20:4792600-4796600	Enhancers	Brain Angular Gyrus	brain
29	chr20:4792800-4796200	Active TSS	Rectal Smooth Muscle	rectum
30	chr20:4793000-4798200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr20:4793400-4796000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
32	chr20:4793600-4796000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr20:4793600-4796400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
34	chr20:4793800-4796000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr20:4794000-4796200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr20:4794000-4796200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr20:4794000-4796600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr20:4794200-4796600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr20:4794400-4796400	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr20:4794400-4796600	Enhancers	Brain Substantia Nigra	brain
41	chr20:4794400-4796600	Genic enhancers	Fetal Muscle Trunk	muscle
42	chr20:4794600-4796000	Flanking Active TSS	Fetal Thymus	thymus
43	chr20:4794600-4796000	Flanking Active TSS	Thymus	Thymus
44	chr20:4794600-4796200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr20:4794600-4796200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr20:4794800-4796000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr20:4794800-4796000	Active TSS	Colonic Mucosa	Colon
48	chr20:4794800-4796200	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr20:4794800-4796600	Enhancers	H1 Cell Line	embryonic stem cell
50	chr20:4794800-4796600	Enhancers	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links