Variant report

Variant	rs4231
Chromosome Location	chr6:33383974-33383975
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr6:33383935-33384600	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:33379963-33384071	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr6:33383899-33384091	HUVEC	blood vessel:	n/a	n/a
4	BATF	chr6:33383862-33384651	GM12878	blood:	n/a	chr6:33384227-33384238
5	POLR2A	chr6:33379970-33384148	GM12878	blood:	n/a	n/a
6	PML	chr6:33383739-33384857	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:33380137-33384099	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr6:33382992-33384068	HepG2	liver:	n/a	n/a
9	POLR2A	chr6:33383025-33386064	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:33380085-33387208	IMR90	lung:	n/a	n/a
11	CHD2	chr6:33383920-33384646	GM12878	blood:	n/a	n/a
12	RUNX3	chr6:33383863-33384762	GM12878	blood:	n/a	n/a
13	IRF4	chr6:33383950-33384665	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:33383588-33384073	K562	blood:	n/a	n/a
15	POLR2A	chr6:33383939-33383976	HepG2	liver:	n/a	n/a
16	POLR2A	chr6:33380060-33386533	K562	blood:	n/a	n/a
17	MTA3	chr6:33383820-33387438	GM12878	blood:	n/a	n/a
18	NFIC	chr6:33383968-33384668	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:33382958-33384048	K562	blood:	n/a	n/a
20	TCF7L2	chr6:33383829-33384109	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr6:33383796-33384817	GM12878	blood:	n/a	n/a
22	MAZ	chr6:33383918-33385164	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:33382713-33386910	GM12878	blood:	n/a	n/a
24	POLR2A	chr6:33380895-33384143	K562	blood:	n/a	n/a
25	POLR2A	chr6:33380002-33384129	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr6:33383678-33383975	GM12878	blood:	n/a	n/a
27	POLR2A	chr6:33383954-33384100	K562	blood:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33279489..33293095-chr6:33375317..33398824,56	K562	blood:
2	chr6:33243299..33244923-chr6:33383429..33386295,2	MCF-7	breast:
3	chr6:33264410..33268847-chr6:33383674..33387403,5	MCF-7	breast:
4	chr6:33382580..33384156-chr6:33587956..33590051,2	K562	blood:
5	chr6:33264378..33268881-chr6:33383627..33388443,14	K562	blood:
6	chr6:33241747..33248128-chr6:33380775..33386072,13	K562	blood:
7	chr6:33383299..33386120-chr6:34202398..34204899,2	K562	blood:
8	chr6:33280795..33292485-chr6:33374786..33387605,31	K562	blood:
9	chr6:33381847..33384907-chr6:33420236..33423106,3	MCF-7	breast:
10	chr6:33237639..33241732-chr6:33383253..33390116,11	K562	blood:
11	chr6:33239271..33241277-chr6:33383669..33386403,3	MCF-7	breast:
12	chr6:33357335..33362175-chr6:33383352..33389421,14	K562	blood:
13	chr6:33242542..33249529-chr6:33381747..33388277,18	K562	blood:
14	chr6:33381203..33384118-chr6:33546265..33549089,2	K562	blood:
15	chr6:33358575..33362850-chr6:33383674..33386989,4	MCF-7	breast:
16	chr6:33371627..33375942-chr6:33381284..33387543,6	K562	blood:
17	chr6:33237802..33241730-chr6:33382199..33389112,10	K562	blood:

No data

Variant related genes	Relation type
SYNGAP1	TF binding region
ENSG00000223501	Chromatin interaction
ENSG00000236104	Chromatin interaction
ENSG00000227057	Chromatin interaction
ENSG00000096433	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000030110	Chromatin interaction
ENSG00000237441	Chromatin interaction
ENSG00000213588	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000204209	Chromatin interaction
ENSG00000235863	Chromatin interaction
ENSG00000137309	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1106606	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11751696	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11753355	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11756267	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11756767	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11757379	1.00[CHB][hapmap]
rs11759285	0.82[EUR][1000 genomes]
rs13195171	1.00[CHB][hapmap]
rs2235982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41267647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41271245	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55699469	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7752202	0.90[EUR][1000 genomes]
rs9277997	0.89[EUR][1000 genomes]
rs9278001	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9278005	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9278006	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9278007	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9278015	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9278016	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9278019	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9278027	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9278028	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9278034	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9278036	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9278038	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9278039	0.85[EUR][1000 genomes]
rs9278040	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9278043	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9278044	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9278045	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9278046	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9278049	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
2	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv885769	chr6:33377522-33412197	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	48 gene(s)	inside rSNPs	diseases
4	nsv602832	chr6:33382241-33520221	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv932196	chr6:33383131-33400706	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4231	CUTA	cis	brain	BrainEAC
rs4231	CUTA	cis	thalamus	BrainEAC
rs4231	CUTA	cis	intralobular white matter	BrainEAC
rs4231	CUTA	cis	putamen	BrainEAC
rs4231	PHF1	cis	temporal cortex	BrainEAC
rs4231	PHF1	cis	brain	BrainEAC

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33379600-33384200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:33379600-33384400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:33379600-33384400	Weak transcription	Fetal Kidney	kidney
4	chr6:33379600-33384400	Weak transcription	Stomach Mucosa	stomach
5	chr6:33379800-33384200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr6:33379800-33384200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:33379800-33384400	Genic enhancers	Primary B cells from peripheral blood	blood
8	chr6:33380000-33384000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:33380000-33384200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:33380000-33384400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:33380000-33384400	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr6:33380000-33384400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
13	chr6:33380000-33384600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
14	chr6:33380200-33384000	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr6:33380200-33384000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:33380200-33384000	Strong transcription	Aorta	Aorta
17	chr6:33380200-33384000	Strong transcription	Brain Substantia Nigra	brain
18	chr6:33380200-33384200	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:33380200-33384400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr6:33380200-33384400	Strong transcription	Brain Inferior Temporal Lobe	brain
21	chr6:33380200-33384800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:33380200-33384800	Genic enhancers	Spleen	Spleen
23	chr6:33380400-33384000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr6:33380400-33384400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
25	chr6:33380400-33384600	Genic enhancers	Primary B cells from cord blood	blood
26	chr6:33380600-33384200	Strong transcription	Primary T cells from cord blood	blood
27	chr6:33380600-33384800	Genic enhancers	Pancreas	Pancrea
28	chr6:33380800-33384200	Strong transcription	Rectal Smooth Muscle	rectum
29	chr6:33381000-33384000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr6:33381000-33384200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr6:33381600-33384200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:33381800-33384400	Strong transcription	Brain Anterior Caudate	brain
33	chr6:33381800-33384400	Genic enhancers	Brain Germinal Matrix	brain
34	chr6:33382000-33384000	Genic enhancers	K562	blood
35	chr6:33382000-33384200	Weak transcription	Psoas Muscle	Psoas
36	chr6:33382000-33384400	Weak transcription	HSMMtube	muscle
37	chr6:33382200-33384200	Genic enhancers	A549	lung
38	chr6:33382200-33385400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:33382400-33384400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:33382400-33384600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:33382600-33384400	Enhancers	Fetal Brain Male	brain
42	chr6:33382600-33384400	Genic enhancers	Monocytes-CD14+_RO01746	blood
43	chr6:33382600-33384600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr6:33382800-33384200	Genic enhancers	Colonic Mucosa	Colon
45	chr6:33382800-33384200	Genic enhancers	Lung	lung
46	chr6:33382800-33384400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr6:33382800-33384400	Genic enhancers	Fetal Intestine Small	intestine
48	chr6:33382800-33384400	Genic enhancers	Fetal Muscle Trunk	muscle
49	chr6:33382800-33384800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:33383000-33384000	Flanking Active TSS	GM12878-XiMat	blood

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