Variant report

Variant	rs1263349
Chromosome Location	chr4:2934308-2934309
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:8)
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	PML	chr4:2934072-2934601	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:2932773-2934678	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:2929559-2936017	GM12878	blood:	n/a	n/a
4	CTCF	chr4:2934280-2934430	GM12867	blood:	n/a	n/a
5	POLR2A	chr4:2932590-2935163	GM18505	blood:	n/a	n/a
6	CTCF	chr4:2934200-2934350	GM12872	blood:	n/a	n/a
7	POLR2A	chr4:2934192-2934615	A549	lung:	n/a	n/a
8	POLR2A	chr4:2932331-2934648	K562	blood:	n/a	n/a
9	POLR2A	chr4:2933146-2935604	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr4:2934005-2934631	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr4:2930058-2935267	GM12892	blood:	n/a	n/a
12	POLR2A	chr4:2934122-2934782	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr4:2929805-2936295	HL-60	blood:	n/a	n/a
14	POLR2A	chr4:2934101-2936177	MCF-7	breast:	n/a	n/a
15	MAX	chr4:2933383-2934333	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:2934108-2934634	GM12892	blood:	n/a	n/a
17	POLR2A	chr4:2930022-2934363	GM12892	blood:	n/a	n/a
18	POLR2A	chr4:2932354-2934493	GM12878	blood:	n/a	n/a
19	POLR2A	chr4:2932735-2936200	U87	brain:	n/a	n/a
20	POLR2A	chr4:2932716-2936132	GM12878	blood:	n/a	n/a
21	POLR2A	chr4:2933173-2934391	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr4:2930118-2940539	K562	blood:	n/a	n/a
23	POLR2A	chr4:2933222-2935217	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr4:2932797-2936194	U87	brain:	n/a	n/a
25	POLR2A	chr4:2932495-2934626	GM12891	blood:	n/a	n/a
26	POLR2A	chr4:2933967-2934324	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr4:2934109-2935469	U87	brain:	n/a	n/a
28	POLR2A	chr4:2932421-2934495	GM12878	blood:	n/a	n/a
29	POLR2A	chr4:2930571-2934637	PFSK-1	brain:	n/a	n/a
30	FOSL2	chr4:2934117-2934769	HepG2	liver:	n/a	n/a
31	POLR2A	chr4:2931577-2935568	PANC-1	pancreas:	n/a	n/a
32	POLR2A	chr4:2932743-2935704	HepG2	liver:	n/a	n/a
33	POLR2A	chr4:2934041-2935445	U87	brain:	n/a	n/a
34	POLR2A	chr4:2930108-2936184	GM12878	blood:	n/a	n/a
35	POLR2A	chr4:2930105-2936184	HL-60	blood:	n/a	n/a
36	POLR2A	chr4:2932413-2934316	GM19193	blood:	n/a	n/a
37	POLR2A	chr4:2934114-2934830	IMR90	lung:	n/a	n/a
38	MTA3	chr4:2932656-2935304	GM12878	blood:	n/a	n/a
39	POLR2A	chr4:2930406-2935196	K562	blood:	n/a	n/a
40	POLR2A	chr4:2932303-2935919	SK-N-MC	brain:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:2903718..2915473-chr4:2930612..2941584,27	MCF-7	breast:
2	chr4:2818050..2820446-chr4:2931198..2934919,4	MCF-7	breast:
3	chr4:2790052..2809152-chr4:2930639..2948075,83	MCF-7	breast:
4	chr4:2866956..2870306-chr4:2932983..2937533,4	K562	blood:
5	chr4:2842030..2853279-chr4:2934021..2940851,24	MCF-7	breast:
6	chr4:2753882..2759883-chr4:2932429..2941474,15	MCF-7	breast:
7	chr4:2747787..2749353-chr4:2932713..2934414,2	MCF-7	breast:
8	chr4:2844667..2846499-chr4:2932403..2934582,2	MCF-7	breast:

No data

Variant related genes	Relation type
MFSD10	TF binding region
NOP14-AS1	TF binding region
ENSG00000087266	Chromatin interaction
ENSG00000087274	Chromatin interaction
ENSG00000168884	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1012365	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1263338	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1263339	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1263342	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1263344	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1263345	0.83[ASW][hapmap];0.94[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1263347	0.83[ASW][hapmap];0.94[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1263359	0.86[CHB][hapmap]
rs1263360	0.91[CHB][hapmap]
rs12642795	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1419045	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16843452	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.94[MEX][hapmap]
rs16843523	0.89[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap]
rs2051560	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2071695	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2097081	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.81[ASN][1000 genomes]
rs2185885	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2237004	0.94[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2239728	0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.90[ASN][1000 genomes]
rs2282772	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2282773	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2282774	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2285084	0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.90[ASN][1000 genomes]
rs2301374	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2798287	0.81[ASN][1000 genomes]
rs3775068	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs3796469	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4690000	0.89[CEU][hapmap]
rs4690001	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.80[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.81[YRI][hapmap]
rs4690065	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4961	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4963	0.94[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4964	0.82[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73189458	0.80[EUR][1000 genomes]
rs762847	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7664801	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1263349	ZFYVE28	cis	parietal	SCAN
rs1263349	DGKQ	cis	parietal	SCAN
rs1263349	ZNF732	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2901200-2934600	Weak transcription	Hela-S3	cervix
2	chr4:2907400-2935400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:2911200-2935000	Weak transcription	Psoas Muscle	Psoas
4	chr4:2912600-2934800	Weak transcription	A549	lung
5	chr4:2913000-2935000	Weak transcription	K562	blood
6	chr4:2924000-2934400	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr4:2924200-2934400	Strong transcription	Fetal Stomach	stomach
8	chr4:2924200-2934800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:2925000-2934400	Strong transcription	Osteobl	bone
10	chr4:2925200-2934800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:2925400-2934400	Strong transcription	NHLF	lung
12	chr4:2925600-2934400	Strong transcription	NHEK	skin
13	chr4:2925800-2935000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr4:2926000-2934400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:2926200-2935000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr4:2926600-2934600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:2926600-2935200	Weak transcription	Fetal Kidney	kidney
18	chr4:2926600-2936600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr4:2927000-2934400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:2927200-2934400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:2927600-2934400	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr4:2928600-2935000	Weak transcription	Small Intestine	intestine
23	chr4:2928600-2935200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
24	chr4:2930000-2934800	Weak transcription	NHDF-Ad	bronchial
25	chr4:2930400-2934400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:2930600-2934400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:2930600-2934600	Strong transcription	Fetal Intestine Large	intestine
28	chr4:2930600-2935200	Genic enhancers	Lung	lung
29	chr4:2930800-2934400	Genic enhancers	Pancreas	Pancrea
30	chr4:2931000-2934800	Strong transcription	Placenta Amnion	Placenta Amnion
31	chr4:2931200-2934400	Genic enhancers	Gastric	stomach
32	chr4:2931400-2935200	Weak transcription	Brain Substantia Nigra	brain
33	chr4:2931800-2935000	Genic enhancers	Fetal Muscle Trunk	muscle
34	chr4:2932000-2934400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
35	chr4:2932000-2934600	Genic enhancers	Right Ventricle	heart
36	chr4:2932000-2934800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr4:2932000-2935000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:2932000-2935000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:2932000-2935000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:2932000-2935200	Genic enhancers	Fetal Muscle Leg	muscle
41	chr4:2932200-2935400	Genic enhancers	Primary B cells from peripheral blood	blood
42	chr4:2932200-2935600	Enhancers	Stomach Mucosa	stomach
43	chr4:2932200-2935800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:2932200-2936000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:2932400-2934800	Weak transcription	Brain Angular Gyrus	brain
46	chr4:2932400-2935000	Weak transcription	Ovary	ovary
47	chr4:2932400-2935200	Weak transcription	Colon Smooth Muscle	Colon
48	chr4:2932600-2934800	Enhancers	Brain Cingulate Gyrus	brain
49	chr4:2932600-2934800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr4:2932600-2935000	Weak transcription	HepG2	liver

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