Variant report

Variant	rs2326550
Chromosome Location	chr20:4796238-4796239
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	MTA3	chr20:4793227-4796576	GM12878	blood:	n/a	n/a
2	POLR2A	chr20:4792105-4796734	GM12892	blood:	n/a	n/a
3	POLR2A	chr20:4796141-4796557	GM12878	blood:	n/a	n/a
4	ELF1	chr20:4794729-4796598	GM12878	blood:	n/a	chr20:4794991-4795002
5	MTA3	chr20:4792292-4796722	GM12878	blood:	n/a	n/a
6	POLR2A	chr20:4792201-4796647	GM12878	blood:	n/a	n/a
7	NFIC	chr20:4793640-4796642	GM12878	blood:	n/a	n/a
8	RELA	chr20:4792744-4796241	GM18951	blood:	n/a	chr20:4795384-4795393 chr20:4795384-4795393 chr20:4795446-4795455 chr20:4795446-4795455
9	POLR2A	chr20:4793406-4796284	GM12878	blood:	n/a	n/a
10	POLR2A	chr20:4792183-4796668	GM18526	blood:	n/a	n/a
11	POLR2A	chr20:4792226-4796866	GM18951	blood:	n/a	n/a
12	POLR2A	chr20:4791978-4796555	GM15510	blood:	n/a	n/a
13	POLR2A	chr20:4793073-4796580	GM12878	blood:	n/a	n/a
14	RELA	chr20:4793082-4796487	GM10847	blood:	n/a	chr20:4795384-4795393 chr20:4795384-4795393 chr20:4795446-4795455 chr20:4795446-4795455
15	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
16	POLR2A	chr20:4792210-4796639	GM12892	blood:	n/a	n/a
17	TBP	chr20:4793222-4796557	GM12878	blood:	n/a	chr20:4793501-4793512
18	POLR2A	chr20:4793274-4796602	GM12878	blood:	n/a	n/a
19	RUNX3	chr20:4793109-4796627	GM12878	blood:	n/a	n/a
20	POLR2A	chr20:4793285-4796580	Raji	blood:	n/a	n/a
21	EBF1	chr20:4792310-4796769	GM12878	blood:	n/a	chr20:4795061-4795070 chr20:4795061-4795071
22	POLR2A	chr20:4792117-4796668	GM19193	blood:	n/a	n/a
23	POLR2A	chr20:4793220-4796563	GM12891	blood:	n/a	n/a
24	PML	chr20:4793232-4796695	GM12878	blood:	n/a	n/a
25	RELA	chr20:4792370-4796654	GM18505	blood:	n/a	chr20:4796605-4796614 chr20:4795384-4795393 chr20:4795384-4795393 chr20:4795446-4795455 chr20:4796605-4796614 chr20:4795446-4795455
26	POLR2A	chr20:4792023-4796566	GM19099	blood:	n/a	n/a
27	POLR2A	chr20:4794758-4796984	HL-60	blood:	n/a	n/a
28	MAX	chr20:4794384-4796693	NB4	blood:	n/a	chr20:4795832-4795841 chr20:4795832-4795841 chr20:4795830-4795843 chr20:4795573-4795583 chr20:4795832-4795841 chr20:4795830-4795843 chr20:4795573-4795583 chr20:4796546-4796557 chr20:4795830-4795843
29	POLR2A	chr20:4792024-4796734	GM12878	blood:	n/a	n/a
30	POLR2A	chr20:4791628-4796664	GM12891	blood:	n/a	n/a
31	POLR2A	chr20:4793309-4796486	GM12892	blood:	n/a	n/a
32	STAT5A	chr20:4792408-4796478	GM12878	blood:	n/a	chr20:4795734-4795757 chr20:4793799-4793807 chr20:4793882-4793894 chr20:4793993-4794005 chr20:4792493-4792505 chr20:4793907-4793918 chr20:4793640-4793652
33	POLR2A	chr20:4793324-4796374	GM12891	blood:	n/a	n/a
34	RELA	chr20:4792437-4796849	GM12891	blood:	n/a	chr20:4796605-4796614 chr20:4795384-4795393 chr20:4795384-4795393 chr20:4795446-4795455 chr20:4796605-4796614 chr20:4795446-4795455
35	EBF1	chr20:4796230-4796658	GM12878	blood:	n/a	n/a
36	RELA	chr20:4792284-4796724	GM19099	blood:	n/a	chr20:4796605-4796614 chr20:4795384-4795393 chr20:4795384-4795393 chr20:4795446-4795455 chr20:4796605-4796614 chr20:4795446-4795455
37	POLR2A	chr20:4792407-4796808	GM12878	blood:	n/a	n/a
38	MYC	chr20:4796169-4796600	NB4	blood:	n/a	chr20:4796546-4796557
39	NFATC1	chr20:4793571-4796446	GM12878	blood:	n/a	chr20:4795461-4795474
40	FOXM1	chr20:4793557-4796259	GM12878	blood:	n/a	n/a
41	POLR2A	chr20:4791930-4796558	GM18505	blood:	n/a	n/a
42	RELA	chr20:4793124-4796595	GM19193	blood:	n/a	chr20:4795384-4795393 chr20:4795384-4795393 chr20:4795446-4795455 chr20:4795446-4795455
43	POLR2A	chr20:4793137-4796633	GM12892	blood:	n/a	n/a
44	POLR2A	chr20:4793326-4796581	GM12891	blood:	n/a	n/a
45	POLR2A	chr20:4792223-4796635	GM12892	blood:	n/a	n/a
46	POLR2A	chr20:4791906-4796781	HL-60	blood:	n/a	n/a
47	WRNIP1	chr20:4792551-4796483	GM12878	blood:	n/a	n/a
48	MAX	chr20:4794894-4796296	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

Variant related genes	Relation type
RASSF2	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13045004	0.96[EUR][1000 genomes]
rs1885306	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1885308	0.96[EUR][1000 genomes]
rs4813721	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7271897	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][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

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:4779200-4797400	Weak transcription	A549	lung
2	chr20:4779200-4802800	Weak transcription	Aorta	Aorta
3	chr20:4782000-4801600	Weak transcription	Fetal Intestine Small	intestine
4	chr20:4783400-4800400	Weak transcription	Fetal Brain Male	brain
5	chr20:4787000-4796400	Weak transcription	Brain Germinal Matrix	brain
6	chr20:4789000-4801200	Weak transcription	Ovary	ovary
7	chr20:4789800-4796600	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr20:4789800-4796800	Genic enhancers	Fetal Muscle Leg	muscle
9	chr20:4790000-4797000	Enhancers	Lung	lung
10	chr20:4790200-4796600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr20:4790200-4796800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr20:4790400-4801400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr20:4791200-4799000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr20:4791600-4796600	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr20:4792000-4796400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr20:4792200-4796600	Flanking Active TSS	GM12878-XiMat	blood
17	chr20:4792400-4796400	Enhancers	HUVEC	blood vessel
18	chr20:4792400-4796600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr20:4792600-4796600	Enhancers	Brain Angular Gyrus	brain
20	chr20:4793000-4798200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr20:4793600-4796400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
22	chr20:4794000-4796600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr20:4794200-4796600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr20:4794400-4796400	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr20:4794400-4796600	Enhancers	Brain Substantia Nigra	brain
26	chr20:4794400-4796600	Genic enhancers	Fetal Muscle Trunk	muscle
27	chr20:4794800-4796600	Enhancers	H1 Cell Line	embryonic stem cell
28	chr20:4794800-4796600	Enhancers	Brain Anterior Caudate	brain
29	chr20:4794800-4801600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr20:4794800-4803000	Weak transcription	Small Intestine	intestine
31	chr20:4795000-4796400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr20:4795000-4796600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr20:4795000-4796800	Enhancers	Brain Cingulate Gyrus	brain
34	chr20:4795200-4801400	Weak transcription	Fetal Lung	lung
35	chr20:4795200-4801600	Weak transcription	Stomach Mucosa	stomach
36	chr20:4795400-4796400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr20:4795400-4796400	Enhancers	Pancreas	Pancrea
38	chr20:4795400-4796600	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr20:4795400-4802400	Weak transcription	Dnd41	blood
40	chr20:4795400-4802600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr20:4795400-4802600	Weak transcription	Right Atrium	heart
42	chr20:4795600-4796600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr20:4795600-4796600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr20:4795600-4800200	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr20:4795600-4801400	Weak transcription	Fetal Brain Female	brain
46	chr20:4795600-4801600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr20:4795600-4802000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr20:4795800-4796400	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr20:4795800-4796400	Weak transcription	Gastric	stomach
50	chr20:4795800-4796400	Weak transcription	Right Ventricle	heart

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