Variant report

Variant	rs1383659
Chromosome Location	chr4:1171112-1171113
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr4:1170939-1171734	MCF10A-Er-Src	breast:	n/a	chr4:1171620-1171630 chr4:1171620-1171630 chr4:1171620-1171630 chr4:1171620-1171630
2	STAT3	chr4:1170961-1171441	MCF10A-Er-Src	breast:	n/a	n/a
3	EBF1	chr4:1171029-1171117	GM12878	blood:	n/a	n/a
4	FOS	chr4:1171045-1171735	MCF10A-Er-Src	breast:	n/a	chr4:1171620-1171630 chr4:1171620-1171630 chr4:1171620-1171630 chr4:1171620-1171630
5	FOS	chr4:1170956-1171711	MCF10A-Er-Src	breast:	n/a	chr4:1171620-1171630 chr4:1171620-1171630 chr4:1171620-1171630 chr4:1171620-1171630
6	MYC	chr4:1170942-1171706	MCF10A-Er-Src	breast:	n/a	chr4:1171282-1171291
7	EP300	chr4:1170980-1171246	GM12878	blood:	n/a	n/a
8	STAT3	chr4:1170974-1171402	MCF10A-Er-Src	breast:	n/a	n/a
9	MAX	chr4:1170863-1171726	NB4	blood:	n/a	chr4:1171282-1171291
10	RUNX3	chr4:1170876-1171289	GM12878	blood:	n/a	n/a
11	MYC	chr4:1170862-1171762	NB4	blood:	n/a	chr4:1171282-1171291
12	FOS	chr4:1170945-1171684	MCF10A-Er-Src	breast:	n/a	chr4:1171620-1171630 chr4:1171620-1171630 chr4:1171620-1171630 chr4:1171620-1171630
13	POLR2A	chr4:1171112-1171711	MCF10A-Er-Src	breast:	n/a	n/a
14	EBF1	chr4:1170855-1171216	GM12878	blood:	n/a	n/a
15	MYC	chr4:1171011-1171769	MCF10A-Er-Src	breast:	n/a	chr4:1171282-1171291
16	RUNX3	chr4:1170877-1171341	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:1161675..1163555-chr4:1169840..1172430,2	MCF-7	breast:
2	chr4:1164336..1166636-chr4:1170930..1173954,3	K562	blood:

Variant related genes	Relation type
SPON2	TF binding region
ENSG00000159674	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10013662	0.94[LWK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11931513	1.00[EUR][1000 genomes]
rs11932895	1.00[EUR][1000 genomes]
rs13115935	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1383658	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1481168	0.81[LWK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs1680075	1.00[EUR][1000 genomes]
rs1680082	1.00[EUR][1000 genomes]
rs17164618	1.00[EUR][1000 genomes]
rs1732105	1.00[EUR][1000 genomes]
rs1871758	0.85[YRI][hapmap]
rs2127911	1.00[EUR][1000 genomes]
rs28750743	0.87[LWK][hapmap]
rs34082974	1.00[EUR][1000 genomes]
rs4336168	1.00[EUR][1000 genomes]
rs4465987	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs4974567	1.00[TSI][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4974580	1.00[EUR][1000 genomes]
rs4974581	1.00[EUR][1000 genomes]
rs4974634	1.00[EUR][1000 genomes]
rs4974635	0.80[YRI][hapmap]
rs4974636	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs4974641	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57461362	1.00[EUR][1000 genomes]
rs59318613	1.00[EUR][1000 genomes]
rs59669372	1.00[EUR][1000 genomes]
rs60410862	1.00[EUR][1000 genomes]
rs6818213	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6834402	1.00[EUR][1000 genomes]
rs6835204	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6836809	0.80[YRI][hapmap]
rs73069991	1.00[EUR][1000 genomes]
rs73069994	1.00[EUR][1000 genomes]
rs73071910	1.00[EUR][1000 genomes]
rs73071925	1.00[EUR][1000 genomes]
rs73073722	1.00[EUR][1000 genomes]
rs73073725	1.00[EUR][1000 genomes]
rs73073727	1.00[EUR][1000 genomes]
rs73073729	1.00[EUR][1000 genomes]
rs73796061	1.00[EUR][1000 genomes]
rs7660109	1.00[EUR][1000 genomes]
rs7676912	0.80[YRI][hapmap]
rs7691582	1.00[EUR][1000 genomes]
rs922697	0.94[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS 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	104 gene(s)	inside rSNPs	diseases
3	nsv1009619	chr4:901897-1215657	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv1003876	chr4:927509-1191316	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1000381	chr4:927509-1198766	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
7	nsv1012892	chr4:1086871-1176630	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv829835	chr4:1097586-1304239	Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
9	nsv878328	chr4:1141573-1990425	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
10	nsv878329	chr4:1147407-1254930	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
11	nsv878330	chr4:1147407-1523930	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
12	nsv519106	chr4:1158991-1174861	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv593276	chr4:1159680-1227469	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv461151	chr4:1159680-1236840	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv593277	chr4:1159680-1236840	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
16	nsv878331	chr4:1159680-1254930	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
17	nsv461152	chr4:1159680-1415698	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
18	nsv593278	chr4:1159680-1415698	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1167000-1174200	Weak transcription	Primary T cells from cord blood	blood
2	chr4:1167200-1172800	Weak transcription	Right Atrium	heart
3	chr4:1167200-1174200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:1167400-1171200	Weak transcription	Brain Anterior Caudate	brain
5	chr4:1167400-1172600	Weak transcription	Lung	lung
6	chr4:1167400-1173400	Enhancers	Fetal Muscle Leg	muscle
7	chr4:1167800-1171200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:1167800-1171200	Weak transcription	Osteobl	bone
9	chr4:1167800-1173800	Enhancers	Liver	Liver
10	chr4:1168000-1172200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:1169800-1173200	Enhancers	Primary T cells fromperipheralblood	blood
12	chr4:1169800-1173200	Enhancers	Fetal Muscle Trunk	muscle
13	chr4:1170000-1171400	Weak transcription	Fetal Intestine Small	intestine
14	chr4:1170200-1171200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr4:1170200-1172600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:1170400-1173400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr4:1170600-1171200	Enhancers	NHEK	skin
18	chr4:1170600-1172800	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr4:1170600-1172800	Enhancers	Spleen	Spleen
20	chr4:1170600-1173000	Enhancers	Left Ventricle	heart
21	chr4:1170600-1173200	Enhancers	Psoas Muscle	Psoas
22	chr4:1170600-1173400	Enhancers	Stomach Mucosa	stomach
23	chr4:1170800-1171200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr4:1170800-1171200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:1170800-1171200	Enhancers	Colon Smooth Muscle	Colon
26	chr4:1170800-1171200	Enhancers	Pancreas	Pancrea
27	chr4:1170800-1171400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:1170800-1171600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:1170800-1171600	Enhancers	Right Ventricle	heart
30	chr4:1170800-1171600	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr4:1170800-1171600	Flanking Active TSS	HepG2	liver
32	chr4:1170800-1171800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:1170800-1171800	Enhancers	Colonic Mucosa	Colon
34	chr4:1170800-1171800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr4:1170800-1172400	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:1170800-1172400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:1170800-1172800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:1170800-1172800	Enhancers	Esophagus	oesophagus
39	chr4:1170800-1172800	Enhancers	HMEC	breast
40	chr4:1170800-1173000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:1170800-1173000	Enhancers	HSMM	muscle
42	chr4:1170800-1173000	Enhancers	HSMMtube	muscle
43	chr4:1170800-1173200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:1170800-1173400	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr4:1171000-1171200	Flanking Active TSS	Hela-S3	cervix
46	chr4:1171000-1171400	Enhancers	Placenta	Placenta
47	chr4:1171000-1171600	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr4:1171000-1171600	Strong transcription	NHLF	lung
49	chr4:1171000-1171800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr4:1171000-1171800	Enhancers	Fetal Heart	heart

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