Variant report

Variant	rs1272043
Chromosome Location	chr4:1190518-1190519
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:1190461-1190535	K562	blood:	n/a	n/a
2	MAX	chr4:1190340-1190568	K562	blood:	n/a	n/a
3	CTCF	chr4:1190480-1190630	WERI-Rb-1	eye:	n/a	n/a
4	CTCF	chr4:1190460-1190610	NB4	blood:	n/a	n/a
5	CTCF	chr4:1190400-1190550	K562	blood:	n/a	n/a
6	CTCF	chr4:1190469-1190572	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr4:1190460-1190610	HEK293	kidney:	n/a	n/a
8	CTCF	chr4:1190400-1190550	Hela-S3	cervix:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:1178221..1180265-chr4:1189709..1191811,2	MCF-7	breast:
2	chr4:1189059..1190794-chr4:1239654..1242349,2	K562	blood:
3	chr4:1184524..1188288-chr4:1189754..1192117,3	MCF-7	breast:
4	chr4:1009769..1012463-chr4:1190367..1192538,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC092535.1-1	chr4:1189571-1193835	NONHSAT094677
2	lnc-AC092535.1-1	chr4:1189572-1191603	NONHSAT094678

No data

Variant related genes	Relation type
SPON2	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10011708	1.00[TSI][hapmap]
rs10013662	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs11932230	1.00[EUR][1000 genomes]
rs1250087	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1250104	1.00[TSI][hapmap]
rs1250127	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1481168	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs1680077	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2127909	1.00[EUR][1000 genomes]
rs28750743	0.89[ASW][hapmap];1.00[MEX][hapmap]
rs4246689	1.00[EUR][1000 genomes]
rs4974567	1.00[ASW][hapmap];1.00[TSI][hapmap]
rs4974626	1.00[EUR][1000 genomes]
rs4974635	0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs4974645	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs57106389	1.00[EUR][1000 genomes]
rs58168130	1.00[EUR][1000 genomes]
rs61053739	1.00[EUR][1000 genomes]
rs6818213	1.00[MEX][hapmap]
rs6835204	1.00[MEX][hapmap]
rs6836809	1.00[ASW][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs6836952	1.00[EUR][1000 genomes]
rs7659524	1.00[EUR][1000 genomes]
rs7676912	1.00[ASW][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs900031	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs922697	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 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	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	nsv461153	chr4:1174861-1254930	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS 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 miRNA target site	46 gene(s)	inside rSNPs	diseases
18	nsv593279	chr4:1174861-1254930	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
19	nsv461154	chr4:1179213-1254930	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
20	nsv593280	chr4:1179213-1254930	Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
21	nsv878332	chr4:1179213-1254930	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1180800-1194000	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr4:1181200-1193400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr4:1181200-1193600	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr4:1181600-1193600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr4:1184400-1194000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:1185000-1204200	Enhancers	Fetal Muscle Leg	muscle
7	chr4:1185800-1196200	Weak transcription	Small Intestine	intestine
8	chr4:1187000-1197200	Weak transcription	HepG2	liver
9	chr4:1187200-1194000	Weak transcription	Esophagus	oesophagus
10	chr4:1187200-1194400	Weak transcription	A549	lung
11	chr4:1188000-1190600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr4:1188000-1193800	Weak transcription	Stomach Mucosa	stomach
13	chr4:1188000-1194400	Weak transcription	Gastric	stomach
14	chr4:1188200-1193600	Weak transcription	Fetal Thymus	thymus
15	chr4:1188200-1194400	Weak transcription	Right Atrium	heart
16	chr4:1188400-1193800	Weak transcription	Fetal Intestine Large	intestine
17	chr4:1188400-1194400	Weak transcription	Left Ventricle	heart
18	chr4:1188600-1190600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:1188600-1190600	Enhancers	Fetal Muscle Trunk	muscle
20	chr4:1188600-1191000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:1188600-1192000	Weak transcription	HSMMtube	muscle
22	chr4:1188600-1192000	Weak transcription	NH-A	brain
23	chr4:1188600-1193400	Weak transcription	Colon Smooth Muscle	Colon
24	chr4:1188600-1193800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr4:1188600-1194200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr4:1188600-1194200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:1188600-1194400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:1188600-1194400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:1188800-1193600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr4:1188800-1194200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:1189200-1190800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:1189200-1191400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr4:1189200-1192000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:1189200-1192000	Weak transcription	HSMM	muscle
35	chr4:1189200-1193400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:1189200-1194000	Weak transcription	Ovary	ovary
37	chr4:1189200-1194400	Weak transcription	Brain Anterior Caudate	brain
38	chr4:1189400-1192000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr4:1189400-1194800	Weak transcription	Brain Hippocampus Middle	brain
40	chr4:1189600-1191000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:1189600-1191000	Genic enhancers	Primary T cells fromperipheralblood	blood
42	chr4:1189600-1191000	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr4:1189600-1191000	Strong transcription	NHLF	lung
44	chr4:1189600-1192000	Strong transcription	Fetal Intestine Small	intestine
45	chr4:1189600-1192200	Strong transcription	Dnd41	blood
46	chr4:1189600-1192600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr4:1189600-1192800	Strong transcription	Primary T cells from cord blood	blood
48	chr4:1189800-1190600	Strong transcription	Colonic Mucosa	Colon
49	chr4:1189800-1190800	Strong transcription	Thymus	Thymus
50	chr4:1189800-1191000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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