Variant report

Variant	rs3820594
Chromosome Location	chr1:155829511-155829512
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	FOXM1	chr1:155829490-155830610	GM12878	blood:	n/a	n/a
2	BHLHE40	chr1:155828858-155830514	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:155829265-155829513	SK-N-SH	brain:	n/a	n/a
4	CEBPB	chr1:155829050-155829791	MCF-7	breast:	n/a	n/a
5	USF2	chr1:155829498-155829589	H1-hESC	embryonic stem cell:	n/a	n/a
6	NR2F2	chr1:155828677-155829542	K562	blood:	n/a	n/a
7	JUN	chr1:155828448-155831227	K562	blood:	n/a	chr1:155830459-155830472 chr1:155829792-155829803
8	REST	chr1:155828738-155831562	H1-neurons	neurons:	n/a	chr1:155830066-155830079 chr1:155829006-155829020 chr1:155830399-155830412
9	YY1	chr1:155829147-155830582	H1-hESC	embryonic stem cell:	n/a	chr1:155830029-155830037 chr1:155830078-155830092 chr1:155829651-155829662 chr1:155830030-155830040 chr1:155830078-155830087 chr1:155830018-155830040 chr1:155830378-155830387
10	STAT5A	chr1:155828806-155830621	GM12878	blood:	n/a	chr1:155829998-155830010 chr1:155829965-155829977 chr1:155829969-155829981
11	POLR2A	chr1:155828760-155830864	U87	brain:	n/a	n/a
12	IRF1	chr1:155828956-155829519	K562	blood:	n/a	chr1:155828977-155828994 chr1:155829102-155829113 chr1:155829045-155829057 chr1:155829046-155829056
13	POLR2A	chr1:155829078-155831211	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAZ	chr1:155828769-155830972	IMR90	lung:	n/a	n/a
15	ELF1	chr1:155828744-155829604	HCT-116	colon:	n/a	chr1:155829213-155829226
16	MTA3	chr1:155829182-155830918	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:155829054-155830756	GM12892	blood:	n/a	n/a
18	FOXM1	chr1:155828772-155829688	GM12878	blood:	n/a	n/a
19	TAF1	chr1:155829081-155830705	H1-neurons	neurons:	n/a	n/a
20	POLR2A	chr1:155828820-155830931	SK-N-SH	brain:	n/a	n/a
21	SIN3AK20	chr1:155828983-155829660	MCF-7	breast:	n/a	n/a
22	RUNX3	chr1:155829412-155830650	GM12878	blood:	n/a	n/a
23	CTBP2	chr1:155829215-155829706	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr1:155828979-155830613	GM18951	blood:	n/a	n/a
25	HDAC2	chr1:155829068-155829603	MCF-7	breast:	n/a	n/a
26	ZEB1	chr1:155829072-155830153	GM12878	blood:	n/a	n/a
27	REST	chr1:155829047-155830622	H1-neurons	neurons:	n/a	chr1:155830066-155830079 chr1:155830399-155830412
28	GABPA	chr1:155828912-155829556	SK-N-SH	brain:	n/a	n/a
29	ELF1	chr1:155828963-155830531	GM12878	blood:	n/a	chr1:155830080-155830092 chr1:155829213-155829226
30	MXI1	chr1:155828036-155831184	SK-N-SH	brain:	n/a	n/a
31	YY1	chr1:155829028-155829583	GM12878	blood:	n/a	n/a
32	CEBPB	chr1:155828657-155829711	HepG2	liver:	n/a	chr1:155828813-155828824
33	KAT2A	chr1:155829393-155829594	GM12878	blood:	n/a	n/a
34	POLR2A	chr1:155828910-155829585	Raji	blood:	n/a	n/a
35	KAP1	chr1:155828875-155829933	U2OS	brain:	n/a	n/a
36	PML	chr1:155828739-155830841	GM12878	blood:	n/a	n/a
37	WRNIP1	chr1:155828908-155829924	GM12878	blood:	n/a	n/a
38	POLR2A	chr1:155828936-155829572	GM19099	blood:	n/a	n/a
39	POLR2A	chr1:155829220-155829535	GM12878	blood:	n/a	n/a
40	POLR2A	chr1:155829232-155830446	GM12891	blood:	n/a	n/a
41	CEBPB	chr1:155829385-155829664	H1-hESC	embryonic stem cell:	n/a	n/a
42	ELF1	chr1:155828821-155829637	MCF-7	breast:	n/a	chr1:155829213-155829226
43	POLR2A	chr1:155828766-155830858	U87	brain:	n/a	n/a
44	HDAC2	chr1:155829171-155829603	HepG2	liver:	n/a	n/a
45	POLR2A	chr1:155829110-155830615	GM12892	blood:	n/a	n/a
46	ELF1	chr1:155828899-155829621	MCF-7	breast:	n/a	chr1:155829213-155829226
47	POLR2A	chr1:155828934-155831031	H1-neurons	neurons:	n/a	n/a
48	POLR2A	chr1:155828955-155830536	GM18526	blood:	n/a	n/a
49	RELA	chr1:155829340-155830515	GM15510	blood:	n/a	n/a
50	CEBPB	chr1:155828644-155829711	K562	blood:	n/a	chr1:155828813-155828824

No.	Distal block	Cell Line	Cell type
1	chr1:155828536..155830676-chr1:155863027..155864768,2	MCF-7	breast:
2	chr1:155827720..155829517-chr1:156180623..156183701,3	K562	blood:
3	chr1:155825368..155829605-chr1:155879516..155883021,7	K562	blood:
4	chr1:155825171..155830547-chr1:155878470..155884979,12	K562	blood:
5	chr1:155827023..155830284-chr1:156022724..156025393,4	K562	blood:

Variant related genes	Relation type
GON4L	TF binding region
ENSG00000260238	Chromatin interaction
ENSG00000143622	Chromatin interaction
ENSG00000116586	Chromatin interaction
ENSG00000160803	Chromatin interaction
ENSG00000201614	Chromatin interaction
ENSG00000160783	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10796955	0.86[MEX][hapmap]
rs10908479	0.92[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap]
rs10908481	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12024257	0.81[AMR][1000 genomes]
rs12035524	0.80[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.81[MKK][hapmap]
rs12037177	0.81[MEX][hapmap]
rs12563627	0.80[JPT][hapmap]
rs12744132	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1749405	0.80[JPT][hapmap]
rs1889532	0.86[MEX][hapmap]
rs2016251	0.91[MEX][hapmap]
rs2282301	0.86[MEX][hapmap]
rs2297649	0.91[MEX][hapmap]
rs2993207	0.80[JPT][hapmap]
rs348196	0.80[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap]
rs3738590	0.92[CEU][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap]
rs475550	0.92[CEU][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap]
rs488079	0.80[JPT][hapmap]
rs625658	0.80[JPT][hapmap]
rs6427286	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs6657670	0.82[AMR][1000 genomes]
rs6667652	0.86[MEX][hapmap]
rs670876	0.80[CHB][hapmap]
rs678157	0.82[JPT][hapmap]
rs708611	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs729022	0.80[JPT][hapmap];0.82[MEX][hapmap]
rs7528441	0.81[AMR][1000 genomes]
rs7541060	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs7556519	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821551	0.84[CHB][hapmap]
rs822478	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs822490	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs822494	0.98[ASN][1000 genomes]
rs822505	0.80[JPT][hapmap]
rs822508	0.80[JPT][hapmap];0.83[MEX][hapmap]
rs860295	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs867549	0.86[MEX][hapmap]
rs867550	0.86[MEX][hapmap]
rs915181	0.86[MEX][hapmap]

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	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1003170	chr1:155762204-155836564	Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs3820594	PRUNE	cis	cerebellum	SCAN
rs3820594	YY1AP1	cis	parietal	SCAN
rs3820594	GPATCH4	cis	parietal	SCAN
rs3820594	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs3820594	SPRR3	cis	parietal	SCAN
rs3820594	RIT1	cis	cerebellum	SCAN
rs3820594	YY1AP1	cis	cerebellum	SCAN
rs3820594	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs3820594	FAM189B	cis	cerebellum	SCAN
rs3820594	GON4L	Cis_1M	lymphoblastoid	RTeQTL
rs3820594	RIT1	cis	Thyroid	GTEx
rs3820594	GBA	cis	Esophagus Mucosa	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155826400-155829600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:155827200-155829600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:155827200-155829800	Flanking Active TSS	Dnd41	blood
4	chr1:155828000-155829600	Active TSS	HepG2	liver
5	chr1:155828200-155829600	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr1:155828200-155830400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr1:155828400-155829600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:155828400-155830600	Active TSS	Psoas Muscle	Psoas
9	chr1:155828400-155831000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:155828600-155829600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:155828600-155829600	Active TSS	Ovary	ovary
12	chr1:155828600-155829600	Active TSS	Rectal Mucosa Donor 31	rectum
13	chr1:155828600-155830000	Active TSS	Thymus	Thymus
14	chr1:155828600-155830200	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr1:155828600-155830600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:155828600-155830600	Active TSS	Brain Anterior Caudate	brain
17	chr1:155828600-155830600	Active TSS	Brain Hippocampus Middle	brain
18	chr1:155828600-155830600	Active TSS	Rectal Smooth Muscle	rectum
19	chr1:155828600-155830800	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr1:155828600-155830800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:155828600-155830800	Active TSS	Fetal Kidney	kidney
22	chr1:155828600-155831000	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr1:155828800-155829600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr1:155828800-155829600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:155828800-155829600	Enhancers	Pancreas	Pancrea
26	chr1:155828800-155830000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr1:155828800-155830400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:155828800-155830400	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr1:155828800-155830400	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr1:155828800-155830600	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr1:155828800-155830600	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr1:155828800-155830600	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr1:155828800-155830600	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr1:155828800-155830600	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr1:155828800-155830600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:155828800-155830600	Flanking Active TSS	Fetal Thymus	thymus
37	chr1:155828800-155830800	Active TSS	H1 Cell Line	embryonic stem cell
38	chr1:155828800-155830800	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr1:155828800-155830800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:155828800-155830800	Active TSS	Aorta	Aorta
41	chr1:155828800-155830800	Active TSS	Brain Angular Gyrus	brain
42	chr1:155828800-155830800	Active TSS	Brain Cingulate Gyrus	brain
43	chr1:155828800-155830800	Active TSS	Brain Substantia Nigra	brain
44	chr1:155828800-155830800	Active TSS	Colonic Mucosa	Colon
45	chr1:155828800-155830800	Active TSS	NHLF	lung
46	chr1:155828800-155831000	Active TSS	Fetal Intestine Large	intestine
47	chr1:155828800-155831200	Active TSS	Fetal Brain Male	brain
48	chr1:155829000-155829600	Active TSS	Osteobl	bone
49	chr1:155829000-155829800	Active TSS	Esophagus	oesophagus
50	chr1:155829000-155830000	Active TSS	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links