Variant report

Variant	rs9444536
Chromosome Location	chr6:88414699-88414700
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr6:88414644-88415454	GM12878	blood:	n/a	n/a
2	EBF1	chr6:88414526-88415288	GM12878	blood:	n/a	n/a
3	CBX3	chr6:88414681-88415354	K562	blood:	n/a	n/a
4	RCOR1	chr6:88414598-88415480	K562	blood:	n/a	n/a
5	BHLHE40	chr6:88414617-88415445	K562	blood:	n/a	n/a
6	TBL1XR1	chr6:88414693-88415422	GM12878	blood:	n/a	n/a
7	BATF	chr6:88414657-88415352	GM12878	blood:	n/a	chr6:88415034-88415045
8	BCLAF1	chr6:88414620-88415618	GM12878	blood:	n/a	chr6:88415136-88415145
9	WRNIP1	chr6:88414498-88415316	GM12878	blood:	n/a	n/a
10	MAX	chr6:88414693-88415328	A549	lung:	n/a	chr6:88415137-88415146
11	SP1	chr6:88414687-88415290	A549	lung:	n/a	n/a
12	NFYB	chr6:88414673-88415321	GM12878	blood:	n/a	n/a
13	FOXM1	chr6:88414549-88415353	GM12878	blood:	n/a	n/a
14	ZNF384	chr6:88414351-88415305	K562	blood:	n/a	n/a
15	TEAD4	chr6:88414566-88415305	K562	blood:	n/a	n/a
16	MTA3	chr6:88414601-88415358	GM12878	blood:	n/a	n/a
17	MTA3	chr6:88414416-88415476	GM12878	blood:	n/a	n/a
18	CREB1	chr6:88414565-88415459	GM12878	blood:	n/a	n/a
19	TBP	chr6:88414658-88415290	GM12878	blood:	n/a	n/a
20	TEAD4	chr6:88414632-88415251	K562	blood:	n/a	n/a
21	STAT5A	chr6:88414662-88415285	GM12878	blood:	n/a	n/a
22	TCF12	chr6:88414692-88415457	A549	lung:	n/a	n/a
23	ZMIZ1	chr6:88414648-88415238	K562	blood:	n/a	n/a
24	SMC3	chr6:88414656-88415326	GM12878	blood:	n/a	n/a
25	ATF2	chr6:88414572-88415628	GM12878	blood:	n/a	n/a
26	RCOR1	chr6:88414586-88415550	IMR90	lung:	n/a	n/a
27	GATA3	chr6:88414649-88415453	A549	lung:	n/a	n/a
28	NFATC1	chr6:88414628-88415349	GM12878	blood:	n/a	n/a
29	RUNX3	chr6:88414517-88415359	GM12878	blood:	n/a	n/a
30	NFIC	chr6:88414471-88415508	GM12878	blood:	n/a	n/a
31	CREB1	chr6:88414660-88415376	K562	blood:	n/a	n/a
32	FOXM1	chr6:88414399-88415424	GM12878	blood:	n/a	n/a
33	NFATC1	chr6:88414626-88415301	GM12878	blood:	n/a	n/a
34	ARID3A	chr6:88414646-88415435	K562	blood:	n/a	n/a
35	EP300	chr6:88414657-88415416	A549	lung:	n/a	n/a
36	RUNX3	chr6:88414460-88415555	GM12878	blood:	n/a	n/a
37	CHD1	chr6:88414586-88415054	GM12878	blood:	n/a	n/a
38	ATF2	chr6:88414637-88415399	GM12878	blood:	n/a	n/a
39	SP1	chr6:88414652-88415382	A549	lung:	n/a	n/a
40	PML	chr6:88414677-88415554	GM12878	blood:	n/a	chr6:88415135-88415144

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:88413588..88415968-chr6:88418558..88420511,2	MCF-7	breast:
2	chr6:88298849..88301180-chr6:88413599..88415307,2	K562	blood:
3	chr6:88409819..88412210-chr6:88413851..88416889,3	MCF-7	breast:

No data

Variant related genes	Relation type
AKIRIN2	TF binding region
ENSG00000146282	Chromatin interaction
ENSG00000135336	Chromatin interaction
ENSG00000135334	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1052623	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1075665	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4707385	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4707386	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58305152	0.82[ASN][1000 genomes]
rs9294384	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9294385	0.96[ASN][1000 genomes]
rs9444531	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9444534	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450760	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9450763	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450773	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450775	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9474	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv2758068	chr6:88358988-88441473	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv2759454	chr6:88358988-88441473	Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9444536	SLC35A1	cis	multi-tissue	Pritchard
rs9444536	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88412800-88414800	Weak transcription	Fetal Intestine Small	intestine
2	chr6:88412800-88414800	Weak transcription	Stomach Mucosa	stomach
3	chr6:88412800-88432600	Weak transcription	Brain Angular Gyrus	brain
4	chr6:88413000-88414800	Weak transcription	NH-A	brain
5	chr6:88413000-88415000	Weak transcription	NHLF	lung
6	chr6:88413000-88415800	Weak transcription	NHDF-Ad	bronchial
7	chr6:88413000-88416000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr6:88413000-88416600	Weak transcription	Fetal Heart	heart
9	chr6:88413000-88416600	Weak transcription	HMEC	breast
10	chr6:88413000-88416800	Weak transcription	HSMM	muscle
11	chr6:88413000-88421600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:88413200-88414800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:88413200-88414800	Weak transcription	Fetal Intestine Large	intestine
14	chr6:88413200-88415000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:88413200-88415200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:88413200-88416400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:88413200-88416600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:88413200-88416600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:88413200-88416600	Weak transcription	Hela-S3	cervix
20	chr6:88413200-88424200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:88413400-88415000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:88413400-88416000	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr6:88413800-88415600	Enhancers	HepG2	liver
24	chr6:88414200-88415600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr6:88414200-88417200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:88414400-88415400	Flanking Active TSS	GM12878-XiMat	blood
27	chr6:88414400-88415600	Enhancers	Osteobl	bone
28	chr6:88414600-88414800	Flanking Active TSS	A549	lung
29	chr6:88414600-88415400	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr6:88414600-88415400	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr6:88414600-88415400	Flanking Active TSS	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links