Variant report

Variant	rs3825073
Chromosome Location	chr11:64900270-64900271
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	POLR2A	chr11:64898630-64903647	GM12891	blood:	n/a	n/a
2	TAL1	chr11:64899952-64900284	K562	blood:	n/a	n/a
3	RELA	chr11:64899715-64901132	GM19193	blood:	n/a	n/a
4	WRNIP1	chr11:64900246-64900296	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:64899927-64901217	GM12892	blood:	n/a	n/a
6	SP1	chr11:64899870-64900328	GM12878	blood:	n/a	chr11:64900180-64900189 chr11:64899979-64899988 chr11:64899896-64899910
7	POLR2A	chr11:64899360-64903246	GM12878	blood:	n/a	n/a
8	POLR2A	chr11:64899478-64901211	GM12892	blood:	n/a	n/a
9	POU2F2	chr11:64899833-64900330	GM12878	blood:	n/a	chr11:64900080-64900090 chr11:64900078-64900093 chr11:64900079-64900090 chr11:64900081-64900091 chr11:64900081-64900089 chr11:64900079-64900090 chr11:64900079-64900092 chr11:64900082-64900089 chr11:64900081-64900090 chr11:64900080-64900092 chr11:64900078-64900092 chr11:64900081-64900091
10	POLR2A	chr11:64898264-64901259	GM12892	blood:	n/a	n/a
11	POLR2A	chr11:64899444-64901145	GM12878	blood:	n/a	n/a
12	ELF1	chr11:64899676-64900350	GM12878	blood:	n/a	n/a
13	POLR2A	chr11:64899997-64900387	GM12891	blood:	n/a	n/a
14	POU2F2	chr11:64899808-64900434	GM12878	blood:	n/a	chr11:64900080-64900090 chr11:64900078-64900093 chr11:64900079-64900090 chr11:64900081-64900091 chr11:64900081-64900089 chr11:64900079-64900090 chr11:64900079-64900092 chr11:64900082-64900089 chr11:64900081-64900090 chr11:64900080-64900092 chr11:64900078-64900092 chr11:64900081-64900091
15	POLR2A	chr11:64899541-64901432	GM18951	blood:	n/a	n/a
16	PML	chr11:64899894-64900378	GM12878	blood:	n/a	n/a
17	RUNX3	chr11:64899839-64901194	GM12878	blood:	n/a	chr11:64900741-64900756
18	PML	chr11:64899772-64900560	GM12878	blood:	n/a	n/a
19	POLR2A	chr11:64899484-64900379	HepG2	liver:	n/a	n/a
20	POLR2A	chr11:64899272-64900384	K562	blood:	n/a	n/a
21	POLR2A	chr11:64898187-64903706	GM12878	blood:	n/a	n/a
22	CEBPB	chr11:64899805-64900353	GM12878	blood:	n/a	n/a
23	POU2F2	chr11:64899784-64900375	GM12891	blood:	n/a	chr11:64900080-64900090 chr11:64900078-64900093 chr11:64900079-64900090 chr11:64900081-64900091 chr11:64900081-64900089 chr11:64900079-64900090 chr11:64900079-64900092 chr11:64900082-64900089 chr11:64900081-64900090 chr11:64900080-64900092 chr11:64900078-64900092 chr11:64900081-64900091
24	POLR2A	chr11:64899473-64903620	Raji	blood:	n/a	n/a
25	RELA	chr11:64899595-64900886	GM12891	blood:	n/a	n/a
26	FOXM1	chr11:64899782-64900765	GM12878	blood:	n/a	n/a
27	EP300	chr11:64899934-64900321	GM12878	blood:	n/a	n/a
28	RUNX3	chr11:64899646-64900335	GM12878	blood:	n/a	n/a
29	NFATC1	chr11:64899868-64900362	GM12878	blood:	n/a	n/a
30	POLR2A	chr11:64899790-64901353	GM12878	blood:	n/a	n/a
31	MEF2A	chr11:64899817-64900401	GM12878	blood:	n/a	n/a
32	POLR2A	chr11:64900140-64901132	K562	blood:	n/a	n/a
33	POLR2A	chr11:64898412-64901302	GM12878	blood:	n/a	n/a
34	BHLHE40	chr11:64899971-64900282	GM12878	blood:	n/a	n/a
35	FOXM1	chr11:64899795-64900356	GM12878	blood:	n/a	n/a
36	MAX	chr11:64899891-64900303	GM12878	blood:	n/a	n/a
37	RELA	chr11:64899791-64900362	GM18951	blood:	n/a	n/a
38	POLR2A	chr11:64899710-64901118	GM10847	blood:	n/a	n/a
39	TCF3	chr11:64899766-64900306	GM12878	blood:	n/a	n/a
40	POU2F2	chr11:64899773-64900362	GM12891	blood:	n/a	chr11:64900080-64900090 chr11:64900078-64900093 chr11:64900079-64900090 chr11:64900081-64900091 chr11:64900081-64900089 chr11:64900079-64900090 chr11:64900079-64900092 chr11:64900082-64900089 chr11:64900081-64900090 chr11:64900080-64900092 chr11:64900078-64900092 chr11:64900081-64900091
41	POLR2A	chr11:64899379-64903136	GM18505	blood:	n/a	n/a
42	POLR2A	chr11:64899641-64901148	GM19099	blood:	n/a	n/a
43	BCLAF1	chr11:64899810-64900441	GM12878	blood:	n/a	n/a
44	POLR2A	chr11:64899670-64901171	GM15510	blood:	n/a	n/a
45	NFIC	chr11:64899836-64900404	GM12878	blood:	n/a	n/a
46	NR2F2	chr11:64899846-64900578	K562	blood:	n/a	n/a
47	STAT1	chr11:64900154-64900345	GM12878	blood:	n/a	chr11:64900171-64900183 chr11:64900175-64900187
48	ELF1	chr11:64899475-64900422	GM12878	blood:	n/a	n/a
49	PAX5	chr11:64899689-64900323	GM12878	blood:	n/a	chr11:64899939-64899958
50	ZEB1	chr11:64899744-64900298	GM12878	blood:	n/a	chr11:64900013-64900020

No.	Distal block	Cell Line	Cell type
1	chr11:64622436..64624370-chr11:64898964..64901159,2	MCF-7	breast:
2	chr11:64577984..64579530-chr11:64899937..64901907,3	K562	blood:
3	chr11:64609880..64612266-chr11:64899287..64901632,2	MCF-7	breast:
4	chr11:64793560..64795544-chr11:64899674..64902650,3	K562	blood:
5	chr11:64899644..64904758-chr11:64914742..64920010,11	K562	blood:
6	chr11:64900106..64905064-chr11:64945207..64950571,10	K562	blood:
7	chr11:64899426..64901940-chr11:64936380..64938384,3	MCF-7	breast:
8	chr11:64642970..64646207-chr11:64900095..64903878,3	K562	blood:
9	chr11:64897351..64905868-chr11:64946257..64954528,24	K562	blood:
10	chr11:64877522..64908330-chr11:64931619..64960265,171	MCF-7	breast:
11	chr11:64899593..64901908-chr11:64970549..64972656,2	MCF-7	breast:
12	chr11:64900055..64903404-chr11:64975247..64978493,3	K562	blood:
13	chr11:64898936..64904142-chr11:64915810..64928732,16	K562	blood:
14	chr11:64899089..64905727-chr11:64934867..64942996,32	K562	blood:
15	chr11:64894864..64904857-chr11:64934599..64944069,37	K562	blood:
16	chr11:64898985..64901826-chr11:64955533..64957107,2	MCF-7	breast:
17	chr11:64863685..64865502-chr11:64899385..64903204,3	K562	blood:
18	chr11:64793895..64795790-chr11:64898693..64901313,2	K562	blood:
19	chr11:64642626..64644470-chr11:64900095..64903022,2	K562	blood:
20	chr11:64899351..64904069-chr11:64950676..64953624,5	K562	blood:
21	chr11:64898025..64904360-chr11:64945543..64952640,32	MCF-7	breast:

Variant related genes	Relation type
SYVN1	TF binding region
ENSG00000255200	Chromatin interaction
ENSG00000014216	Chromatin interaction
ENSG00000204710	Chromatin interaction
ENSG00000255058	Chromatin interaction
ENSG00000110025	Chromatin interaction
ENSG00000110047	Chromatin interaction
ENSG00000270775	Chromatin interaction
ENSG00000249251	Chromatin interaction
ENSG00000133895	Chromatin interaction
ENSG00000222477	Chromatin interaction
ENSG00000171219	Chromatin interaction
ENSG00000254614	Chromatin interaction
ENSG00000149823	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10895986	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227118	0.86[CHB][hapmap]
rs11227120	0.92[CHB][hapmap]
rs11227131	0.96[ASN][1000 genomes]
rs11227137	0.80[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11231929	0.86[CHB][hapmap]
rs1196048	0.86[CHB][hapmap]
rs17743381	0.89[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2282498	0.86[CHB][hapmap]
rs3802936	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[ASN][1000 genomes]
rs3862374	0.86[CHB][hapmap]
rs477539	0.86[CHB][hapmap]
rs489489	0.86[CHB][hapmap]
rs548150	0.86[CHB][hapmap]
rs55646096	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs564476	0.87[MKK][hapmap]
rs564966	0.86[CHB][hapmap]
rs653111	0.86[CHB][hapmap]
rs6591177	0.80[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7124215	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7128220	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72932851	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7943007	0.86[CHB][hapmap]
rs9971546	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv897711	chr11:64772545-64900270	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3825073	PPP1CA	cis	cerebellum	SCAN
rs3825073	RAB1B	cis	parietal	SCAN
rs3825073	FRMD8	cis	cerebellum	SCAN
rs3825073	HRASLS5	cis	cerebellum	SCAN
rs3825073	SPDYC	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64890200-64900600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:64890200-64900800	Weak transcription	Right Atrium	heart
3	chr11:64891600-64900400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr11:64891600-64900400	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr11:64891800-64900400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:64891800-64900400	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr11:64891800-64900400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr11:64891800-64900400	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr11:64891800-64900400	Strong transcription	Ovary	ovary
10	chr11:64891800-64900400	Strong transcription	Thymus	Thymus
11	chr11:64891800-64900400	Strong transcription	A549	lung
12	chr11:64891800-64900600	Strong transcription	Brain Inferior Temporal Lobe	brain
13	chr11:64892000-64900400	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr11:64892000-64900400	Strong transcription	Aorta	Aorta
15	chr11:64892000-64900400	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr11:64892000-64900400	Strong transcription	HSMM	muscle
17	chr11:64892000-64900600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
18	chr11:64897000-64901600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr11:64897600-64900400	Genic enhancers	Spleen	Spleen
20	chr11:64897600-64900600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr11:64897600-64900600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr11:64897800-64900600	Weak transcription	Psoas Muscle	Psoas
23	chr11:64898200-64900600	Genic enhancers	Fetal Muscle Trunk	muscle
24	chr11:64898400-64900600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
25	chr11:64898600-64900800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:64898800-64900400	Genic enhancers	Right Ventricle	heart
27	chr11:64898800-64900800	Genic enhancers	Primary T cells fromperipheralblood	blood
28	chr11:64899000-64900400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr11:64899000-64900800	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
30	chr11:64899200-64900400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:64899200-64900600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr11:64899200-64900600	Weak transcription	Fetal Kidney	kidney
33	chr11:64899200-64900800	Genic enhancers	Brain Cingulate Gyrus	brain
34	chr11:64899400-64900400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:64899400-64900400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr11:64899400-64900400	Weak transcription	Fetal Brain Male	brain
37	chr11:64899400-64900400	Genic enhancers	Hela-S3	cervix
38	chr11:64899400-64900600	Genic enhancers	Fetal Muscle Leg	muscle
39	chr11:64899400-64900600	Genic enhancers	Gastric	stomach
40	chr11:64899400-64900600	Genic enhancers	Stomach Mucosa	stomach
41	chr11:64899400-64900800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr11:64899400-64901000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
43	chr11:64899600-64900400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr11:64899600-64900400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr11:64899600-64900400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr11:64899600-64900400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr11:64899600-64900400	Genic enhancers	Esophagus	oesophagus
48	chr11:64899600-64900600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:64899600-64900600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr11:64899600-64900600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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