Variant report

Variant	rs57890261
Chromosome Location	chr4:1197722-1197723
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POU2F2	chr4:1197237-1197806	GM12878	blood:	n/a	n/a
2	MTA3	chr4:1197229-1197792	GM12878	blood:	n/a	n/a
3	CHD2	chr4:1197259-1197736	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:1197694-1199659	HepG2	liver:	n/a	n/a
5	RUNX3	chr4:1197244-1197786	GM12878	blood:	n/a	n/a
6	IRF4	chr4:1197225-1197779	GM12878	blood:	n/a	n/a
7	STAT5A	chr4:1197304-1197729	GM12878	blood:	n/a	n/a
8	EP300	chr4:1197251-1198033	GM12878	blood:	n/a	n/a
9	ZNF384	chr4:1197313-1197792	GM12878	blood:	n/a	n/a
10	MAX	chr4:1197445-1197905	NB4	blood:	n/a	n/a
11	ATF2	chr4:1197285-1197761	GM12878	blood:	n/a	n/a
12	STAT3	chr4:1197383-1197750	GM12878	blood:	n/a	n/a
13	PAX5	chr4:1197166-1197818	GM12878	blood:	n/a	n/a
14	POU2F2	chr4:1197302-1197738	GM12891	blood:	n/a	n/a
15	MAX	chr4:1197196-1197839	GM12878	blood:	n/a	n/a
16	USF2	chr4:1197240-1197830	GM12878	blood:	n/a	n/a
17	RUNX3	chr4:1197188-1198012	GM12878	blood:	n/a	n/a
18	EP300	chr4:1197207-1197749	GM12878	blood:	n/a	n/a
19	BHLHE40	chr4:1197268-1197982	GM12878	blood:	n/a	n/a
20	POU2F2	chr4:1197310-1197762	GM12878	blood:	n/a	n/a
21	POU2F2	chr4:1197387-1197745	GM12891	blood:	n/a	n/a
22	EBF1	chr4:1197103-1197835	GM12878	blood:	n/a	chr4:1197571-1197582
23	TBL1XR1	chr4:1197262-1197726	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:1195937..1198894-chr4:1221468..1224458,3	K562	blood:
2	chr4:1196184..1198121-chr4:1199420..1202369,2	K562	blood:
3	chr4:1192255..1195518-chr4:1197581..1201308,4	MCF-7	breast:
4	chr4:1195791..1198447-chr4:1208482..1210775,2	MCF-7	breast:

No data

Variant related genes	Relation type
SPON2	TF binding region
ENSG00000159674	Chromatin interaction
ENSG00000159692	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1009901	0.86[ASN][1000 genomes]
rs13115903	0.82[ASN][1000 genomes]
rs17164549	0.81[ASN][1000 genomes]
rs2011161	0.84[ASN][1000 genomes]
rs2178443	0.81[ASN][1000 genomes]
rs2279280	0.82[ASN][1000 genomes]
rs3729593	0.86[ASN][1000 genomes]
rs3733340	0.86[ASN][1000 genomes]
rs3755919	0.83[ASN][1000 genomes]
rs3755931	0.84[ASN][1000 genomes]
rs3755936	0.86[ASN][1000 genomes]
rs3755937	0.86[ASN][1000 genomes]
rs3755943	0.86[ASN][1000 genomes]
rs3755950	0.87[ASN][1000 genomes]
rs3775106	0.86[ASN][1000 genomes]
rs3775109	0.88[ASN][1000 genomes]
rs3892033	0.86[ASN][1000 genomes]
rs55877603	0.81[ASN][1000 genomes]
rs57276390	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57560821	0.86[ASN][1000 genomes]
rs59717591	0.81[ASN][1000 genomes]
rs60846075	0.86[ASN][1000 genomes]
rs61010940	0.86[ASN][1000 genomes]
rs6840663	0.88[ASN][1000 genomes]
rs6856873	0.86[ASN][1000 genomes]
rs73069911	0.87[ASN][1000 genomes]
rs73793112	0.91[ASN][1000 genomes]
rs73793144	0.84[ASN][1000 genomes]
rs73793145	0.86[ASN][1000 genomes]
rs73793148	0.86[ASN][1000 genomes]
rs73793154	0.86[ASN][1000 genomes]
rs73793165	0.83[ASN][1000 genomes]
rs73793175	0.81[ASN][1000 genomes]
rs877987	0.89[ASN][1000 genomes]
rs900030	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	nsv997971	chr4:1191256-1518521	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
22	nsv878333	chr4:1193832-1254930	Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS 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:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1185000-1204200	Enhancers	Fetal Muscle Leg	muscle
2	chr4:1194200-1207800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:1194600-1201600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:1194600-1202400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr4:1194800-1199600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:1194800-1200400	Weak transcription	Ovary	ovary
7	chr4:1194800-1201400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:1194800-1201800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr4:1194800-1201800	Weak transcription	Osteobl	bone
10	chr4:1194800-1202000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:1194800-1203000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:1194800-1203400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr4:1195000-1198000	Enhancers	Fetal Stomach	stomach
14	chr4:1195000-1201400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:1195000-1201600	Weak transcription	Right Atrium	heart
16	chr4:1195200-1198200	Weak transcription	Stomach Mucosa	stomach
17	chr4:1195200-1198400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:1195200-1200000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:1195200-1200600	Weak transcription	Pancreas	Pancrea
20	chr4:1195200-1201200	Enhancers	Spleen	Spleen
21	chr4:1195200-1201400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:1195200-1201600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:1195200-1201600	Weak transcription	Right Ventricle	heart
24	chr4:1195200-1202600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:1195200-1204400	Weak transcription	HMEC	breast
26	chr4:1195200-1214600	Weak transcription	A549	lung
27	chr4:1195400-1198000	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr4:1195400-1198800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr4:1195400-1199600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr4:1195800-1198200	Enhancers	Fetal Intestine Large	intestine
31	chr4:1195800-1201000	Weak transcription	Fetal Brain Female	brain
32	chr4:1196000-1199000	Enhancers	Primary B cells from peripheral blood	blood
33	chr4:1196200-1198000	Enhancers	Duodenum Mucosa	Duodenum
34	chr4:1196200-1198000	Genic enhancers	Fetal Intestine Small	intestine
35	chr4:1196200-1198400	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr4:1196400-1198000	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr4:1196400-1198400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr4:1196400-1198400	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr4:1196400-1198400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr4:1196400-1198800	Weak transcription	Adipose Nuclei	Adipose
41	chr4:1196400-1199200	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr4:1196400-1200800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr4:1196400-1201600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:1196400-1203000	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr4:1196400-1203200	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr4:1196400-1209800	Weak transcription	Primary B cells from cord blood	blood
47	chr4:1196600-1198000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr4:1196600-1198000	Weak transcription	Liver	Liver
49	chr4:1196600-1198000	Weak transcription	HSMMtube	muscle
50	chr4:1196600-1198000	Weak transcription	NHDF-Ad	bronchial

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