Variant report

Variant	rs9461536
Chromosome Location	chr6:29520464-29520465
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:39)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:39 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr6:29520397-29520724	K562	blood:	n/a	n/a
2	GTF2F1	chr6:29520414-29520641	K562	blood:	n/a	n/a
3	ZNF143	chr6:29520404-29520648	GM12878	blood:	n/a	n/a
4	RFX5	chr6:29520322-29520761	Hela-S3	cervix:	n/a	n/a
5	SRF	chr6:29520354-29520603	GM12878	blood:	n/a	n/a
6	SRF	chr6:29520250-29520752	ECC-1	luminal epithelium:	n/a	n/a
7	ZNF143	chr6:29520453-29520722	K562	blood:	n/a	n/a
8	IRF3	chr6:29520412-29520679	GM12878	blood:	n/a	n/a
9	SP1	chr6:29520394-29520745	GM12878	blood:	n/a	n/a
10	RFX5	chr6:29519666-29521148	SK-N-SH	brain:	n/a	n/a
11	STAT3	chr6:29520404-29520772	MCF10A-Er-Src	breast:	n/a	n/a
12	NFYB	chr6:29520289-29520739	GM12878	blood:	n/a	n/a
13	ATF1	chr6:29520358-29520724	K562	blood:	n/a	n/a
14	RFX5	chr6:29519835-29521028	K562	blood:	n/a	n/a
15	BHLHE40	chr6:29520412-29520729	K562	blood:	n/a	n/a
16	CREB1	chr6:29520295-29520739	ECC-1	luminal epithelium:	n/a	n/a
17	SP1	chr6:29520279-29520774	H1-hESC	embryonic stem cell:	n/a	n/a
18	SRF	chr6:29520289-29520672	H1-hESC	embryonic stem cell:	n/a	n/a
19	SRF	chr6:29520372-29520555	GM12878	blood:	n/a	n/a
20	SRF	chr6:29520118-29520806	MCF-7	breast:	n/a	n/a
21	NFYA	chr6:29520439-29520739	Hela-S3	cervix:	n/a	chr6:29520538-29520556
22	RFX5	chr6:29519591-29522025	IMR90	lung:	n/a	n/a
23	NFYA	chr6:29520222-29520731	GM12878	blood:	n/a	chr6:29520538-29520556
24	CREB1	chr6:29520248-29520847	K562	blood:	n/a	n/a
25	ELK1	chr6:29520453-29520819	GM12878	blood:	n/a	n/a
26	RFX5	chr6:29520303-29520805	HepG2	liver:	n/a	n/a
27	CREB1	chr6:29520287-29520807	GM12878	blood:	n/a	n/a
28	STAT3	chr6:29520427-29520715	GM12878	blood:	n/a	n/a
29	BHLHE40	chr6:29520417-29520687	GM12878	blood:	n/a	n/a
30	SRF	chr6:29520196-29520816	HCT-116	colon:	n/a	n/a
31	RFX5	chr6:29519768-29521722	H1-hESC	embryonic stem cell:	n/a	n/a
32	SRF	chr6:29520260-29520764	HCT-116	colon:	n/a	n/a
33	STAT1	chr6:29520258-29521044	Hela-S3	cervix:	n/a	n/a
34	RFX5	chr6:29520212-29520926	GM12878	blood:	n/a	n/a
35	SRF	chr6:29520270-29520797	MCF-7	breast:	n/a	n/a
36	CREB1	chr6:29520423-29520766	H1-hESC	embryonic stem cell:	n/a	n/a
37	CREB1	chr6:29520361-29520866	H1-hESC	embryonic stem cell:	n/a	n/a
38	CREB1	chr6:29520253-29520776	GM12878	blood:	n/a	n/a
39	NFYA	chr6:29520277-29520723	K562	blood:	n/a	chr6:29520538-29520556

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29520442..29521980-chr6:29599358..29601313,2	MCF-7	breast:

No data

Variant related genes	Relation type
OR2I1P	TF binding region
ENSG00000204681	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11970406	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970429	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11970475	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16895067	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16895070	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17184255	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2076484	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2076486	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2076487	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2272991	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2294744	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2294746	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3025657	0.82[ASN][1000 genomes]
rs3025669	0.82[ASN][1000 genomes]
rs362531	0.85[ASN][1000 genomes]
rs362532	0.85[ASN][1000 genomes]
rs57241384	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58008302	0.82[ASN][1000 genomes]
rs59731351	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59802757	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60219685	0.82[ASN][1000 genomes]
rs64036	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456964	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6908631	0.82[ASN][1000 genomes]
rs6913746	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6915177	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6920668	0.82[ASN][1000 genomes]
rs6931702	0.82[ASN][1000 genomes]
rs6933331	0.82[ASN][1000 genomes]
rs73402729	0.87[EUR][1000 genomes]
rs73402731	0.81[EUR][1000 genomes]
rs73402733	0.87[EUR][1000 genomes]
rs73402748	0.82[ASN][1000 genomes]
rs73402770	0.82[ASN][1000 genomes]
rs73402788	0.85[ASN][1000 genomes]
rs7739905	0.82[ASN][1000 genomes]
rs7757931	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9258130	0.82[ASN][1000 genomes]
rs9258132	0.82[ASN][1000 genomes]
rs9461538	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9468551	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9501677	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[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	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9461536	ZNRD1	cis	lymphoblastoid	seeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29515200-29521000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:29520200-29520600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
3	chr6:29520400-29520600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr6:29520400-29520600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
5	chr6:29520400-29520600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr6:29520400-29520600	Bivalent/Poised TSS	Primary B cells from cord blood	blood
7	chr6:29520400-29520600	Active TSS	Primary hematopoietic stem cells	blood
8	chr6:29520400-29520600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:29520400-29520600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:29520400-29520600	Active TSS	Adipose Nuclei	Adipose
11	chr6:29520400-29520600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
12	chr6:29520400-29520600	Enhancers	Colon Smooth Muscle	Colon
13	chr6:29520400-29520600	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr6:29520400-29520800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr6:29520400-29520800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr6:29520400-29520800	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood
17	chr6:29520400-29521000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
18	chr6:29520400-29521400	Bivalent Enhancer	Fetal Heart	heart
19	chr6:29520400-29522000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell

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