Variant report

Variant	rs234263
Chromosome Location	chr5:68387064-68387065
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr5:68386984-68387442	K562	blood:	n/a	n/a
2	EP300	chr5:68387033-68387389	SK-N-SH_RA	brain:	n/a	n/a
3	TBL1XR1	chr5:68387039-68387391	K562	blood:	n/a	n/a
4	PBX3	chr5:68387033-68387526	SK-N-SH	brain:	n/a	n/a
5	JUND	chr5:68387061-68387466	K562	blood:	n/a	n/a
6	RUNX3	chr5:68386913-68387410	GM12878	blood:	n/a	n/a
7	NFIC	chr5:68386921-68387572	SK-N-SH	brain:	n/a	n/a
8	YY1	chr5:68386978-68387198	GM12891	blood:	n/a	n/a
9	RCOR1	chr5:68387019-68387576	K562	blood:	n/a	n/a
10	YY1	chr5:68386919-68387171	GM12892	blood:	n/a	n/a
11	YY1	chr5:68386902-68387172	GM12878	blood:	n/a	n/a
12	YY1	chr5:68386923-68387176	GM12878	blood:	n/a	n/a
13	RUNX3	chr5:68386910-68387338	GM12878	blood:	n/a	n/a
14	BATF	chr5:68386921-68387302	GM12878	blood:	n/a	n/a
15	YY1	chr5:68386908-68387165	K562	blood:	n/a	n/a
16	POLR2A	chr5:68387035-68387550	PBDE	blood:	n/a	n/a
17	GATA1	chr5:68386934-68387637	PBDE	blood:	n/a	n/a
18	YY1	chr5:68386947-68387160	SK-N-SH_RA	brain:	n/a	n/a
19	TCF12	chr5:68386935-68387579	SK-N-SH	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:68387033-68387083	HIPEpiC	eye:	n/a
2	chr5:68387033-68387083	Hepatocyte	liver:	n/a
3	chr5:68387033-68387083	NB4	blood:	n/a
4	chr5:68387033-68387083	NT2-D1	testis:	n/a
5	chr5:68387033-68387083	HEEpiC	esophagus:	n/a
6	chr5:68387033-68387083	HepG2	liver:	n/a
7	chr5:68387033-68387083	HNPCEpiC	eye:	n/a
8	chr5:68387033-68387083	U87	brain:	n/a
9	chr5:68387033-68387083	A549	lung:	n/a
10	chr5:68387033-68387083	Jurkat	blood:	n/a
11	chr5:68387033-68387083	HUVEC	blood vessel:	n/a
12	chr5:68387033-68387083	HCM	heart:	n/a
13	chr5:68387033-68387083	LNCaP	prostate:	n/a
14	chr5:68387033-68387083	ProgFib	skin:	n/a
15	chr5:68387033-68387083	MCF10A-Er-Src	breast:	n/a
16	chr5:68387033-68387083	NH-A	brain:	n/a
17	chr5:68387033-68387083	Hela-S3	cervix:	n/a
18	chr5:68387033-68387083	HCT-116	colon:	n/a
19	chr5:68387033-68387083	HRPEpiC	eye:	n/a
20	chr5:68387033-68387083	AG04449	skin:	fetal
21	chr5:68387033-68387083	PANC-1	pancreas:	n/a
22	chr5:68387033-68387083	AG10803	skin:	n/a
23	chr5:68387033-68387083	CMK	blood:	n/a
24	chr5:68387033-68387083	IMR90	lung:	fetal
25	chr5:68387033-68387083	ECC-1	luminal epithelium:	n/a
26	chr5:68387033-68387083	MCF-7	breast:	n/a
27	chr5:68387033-68387083	BE2_C	brain:	n/a
28	chr5:68387033-68387083	NHDF-neo	bronchial:	n/a
29	chr5:68387033-68387083	K562	blood:	n/a
30	chr5:68387033-68387083	GM19239	blood:	n/a
31	chr5:68387033-68387083	AG04450	lung:	fetal
32	chr5:68387033-68387083	BJ	skin:	n/a
33	chr5:68387033-68387083	HMEC	breast:	n/a
34	chr5:68387033-68387083	SAEC	small airway:	n/a
35	chr5:68387033-68387083	SK-N-MC	brain:	n/a
36	chr5:68387033-68387083	AG09309	skin:	n/a
37	chr5:68387033-68387083	HAEpiC	amniotic membrane:	n/a
38	chr5:68387033-68387083	HEK293	kidney:	embryo
39	chr5:68387033-68387083	HRE	kidney:	n/a
40	chr5:68387033-68387083	SK-N-SH	brain:	n/a
41	chr5:68387033-68387083	ovcar-3	ovarian:	n/a
42	chr5:68387033-68387083	SK-N-SH_RA	brain:	n/a
43	chr5:68387033-68387083	RPTEC	kidney:	n/a
44	chr5:68387033-68387083	HCF	heart:	n/a
45	chr5:68387033-68387083	AG09319	gingival:	n/a
46	chr5:68387033-68387083	T-47D	breast:	n/a
47	chr5:68387033-68387083	GM06990	blood:	n/a
48	chr5:68387033-68387083	SKMC	muscle:	n/a
49	chr5:68387033-68387083	H1-hESC	embryonic stem cell:	embryo
50	chr5:68387033-68387083	AoSMC	blood vessel:	n/a

No data

Variant related genes	Relation type
SLC30A5	TF binding region
SLC30A5	CpG island

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10214127	0.82[CHB][hapmap]
rs164392	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs170893	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs337250	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs337252	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs337257	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs337258	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337260	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449607	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs52131	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv3391099	chr5:68377245-68400350	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
3	nsv881765	chr5:68379836-68448694	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs234263	SLC30A5	cis	brain	BrainEAC

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68381200-68389400	Weak transcription	HUVEC	blood vessel
2	chr5:68382400-68389800	Weak transcription	Right Atrium	heart
3	chr5:68385800-68387800	Enhancers	Fetal Heart	heart
4	chr5:68386200-68389400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:68386400-68387600	Enhancers	GM12878-XiMat	blood
6	chr5:68386400-68389400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:68386400-68389400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr5:68386400-68389400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr5:68387000-68387200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:68387000-68387200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:68387000-68387200	Enhancers	Liver	Liver
12	chr5:68387000-68387200	Enhancers	A549	lung
13	chr5:68387000-68387400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:68387000-68387400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:68387000-68387400	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr5:68387000-68387400	Enhancers	HMEC	breast
17	chr5:68387000-68387400	Flanking Active TSS	K562	blood
18	chr5:68387000-68387400	Enhancers	NHEK	skin
19	chr5:68387000-68387600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:68387000-68387600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr5:68387000-68387600	Enhancers	Right Ventricle	heart
22	chr5:68387000-68387600	Enhancers	HSMM	muscle
23	chr5:68387000-68388000	Enhancers	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links