Variant report

Variant	rs445160
Chromosome Location	chr4:2813503-2813504
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr4:2813484-2814755	ECC-1	luminal epithelium:	n/a	chr4:2814485-2814495 chr4:2814277-2814286
2	NFIC	chr4:2813408-2814342	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr4:2813394-2815108	GM12892	blood:	n/a	n/a
4	RELA	chr4:2813503-2814269	GM18951	blood:	n/a	n/a
5	ZNF263	chr4:2813465-2815744	HEK293-T-REx	kidney:	n/a	chr4:2813988-2813997
6	POLR2A	chr4:2813372-2814453	PFSK-1	brain:	n/a	n/a
7	RUNX3	chr4:2813383-2814467	GM12878	blood:	n/a	n/a
8	POLR2A	chr4:2813485-2814285	GM12892	blood:	n/a	n/a
9	MTA3	chr4:2813221-2816423	GM12878	blood:	n/a	n/a
10	POLR2A	chr4:2813291-2814441	ECC-1	luminal epithelium:	n/a	n/a
11	TCF12	chr4:2813379-2814364	ECC-1	luminal epithelium:	n/a	chr4:2813598-2813608
12	GABPA	chr4:2813333-2814311	HL-60	blood:	n/a	n/a
13	MAX	chr4:2813359-2814594	ECC-1	luminal epithelium:	n/a	chr4:2814485-2814495 chr4:2814277-2814286
14	PAX5	chr4:2813460-2814384	GM12878	blood:	n/a	chr4:2814325-2814334 chr4:2813930-2813939
15	POLR2A	chr4:2813327-2814450	HL-60	blood:	n/a	n/a
16	POLR2A	chr4:2813221-2814866	GM12878	blood:	n/a	n/a
17	EBF1	chr4:2813353-2814269	GM12878	blood:	n/a	n/a
18	POLR2A	chr4:2813498-2814777	GM12892	blood:	n/a	n/a
19	TCF12	chr4:2813251-2814371	ECC-1	luminal epithelium:	n/a	chr4:2813598-2813608
20	CEBPB	chr4:2813470-2814188	GM12878	blood:	n/a	n/a
21	PML	chr4:2813463-2814321	GM12878	blood:	n/a	n/a
22	EP300	chr4:2813426-2814389	ECC-1	luminal epithelium:	n/a	chr4:2813971-2813980 chr4:2814010-2814026
23	POLR2A	chr4:2813477-2814361	HUVEC	blood vessel:	n/a	n/a
24	NR2F2	chr4:2813393-2813979	MCF-7	breast:	n/a	n/a
25	RUNX3	chr4:2813470-2814290	GM12878	blood:	n/a	n/a
26	POLR2A	chr4:2813371-2815082	HUVEC	blood vessel:	n/a	n/a
27	SPI1	chr4:2813481-2814293	HL-60	blood:	n/a	chr4:2813971-2813980
28	STAT5A	chr4:2813465-2814271	GM12878	blood:	n/a	chr4:2813974-2813981 chr4:2813928-2813936
29	EBF1	chr4:2813422-2814116	GM12878	blood:	n/a	n/a
30	ELF1	chr4:2813378-2815264	GM12878	blood:	n/a	chr4:2813926-2813939 chr4:2814001-2814013 chr4:2813969-2813980 chr4:2815005-2815017
31	POLR2A	chr4:2813501-2814475	GM12878	blood:	n/a	n/a
32	POLR2A	chr4:2811919-2815260	HL-60	blood:	n/a	n/a
33	POLR2A	chr4:2813442-2815569	GM12891	blood:	n/a	n/a
34	POLR2A	chr4:2813349-2814460	GM12892	blood:	n/a	n/a
35	MAX	chr4:2813437-2815204	NB4	blood:	n/a	chr4:2814485-2814495 chr4:2814277-2814286
36	MYC	chr4:2813390-2814360	NB4	blood:	n/a	chr4:2814277-2814286

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:2813458-2813508	HCT-116	colon:	n/a
2	chr4:2813458-2813508	SK-N-SH_RA	brain:	n/a
3	chr4:2813458-2813508	GM06990	blood:	n/a
4	chr4:2813458-2813508	AoSMC	blood vessel:	n/a
5	chr4:2813458-2813508	HL-60	blood:	n/a
6	chr4:2813458-2813508	HRE	kidney:	n/a
7	chr4:2813458-2813508	RPTEC	kidney:	n/a
8	chr4:2813458-2813508	H1-hESC	embryonic stem cell:	embryo
9	chr4:2813458-2813508	NH-A	brain:	n/a
10	chr4:2813458-2813508	SAEC	small airway:	n/a
11	chr4:2813458-2813508	NHDF-neo	bronchial:	n/a
12	chr4:2813458-2813508	BJ	skin:	n/a
13	chr4:2813458-2813508	AG04449	skin:	fetal
14	chr4:2813458-2813508	PrEC	prostate:	n/a
15	chr4:2813458-2813508	AG09319	gingival:	n/a
16	chr4:2813458-2813508	Hela-S3	cervix:	n/a
17	chr4:2813458-2813508	SK-N-SH	brain:	n/a
18	chr4:2813458-2813508	AG09309	skin:	n/a
19	chr4:2813458-2813508	HRPEpiC	eye:	n/a
20	chr4:2813458-2813508	GM12891	blood:	n/a
21	chr4:2813458-2813508	Jurkat	blood:	n/a
22	chr4:2813458-2813508	HRCEpiC	kidney:	n/a
23	chr4:2813458-2813508	GM19239	blood:	n/a
24	chr4:2813458-2813508	Hepatocyte	liver:	n/a
25	chr4:2813458-2813508	T-47D	breast:	n/a
26	chr4:2813458-2813508	HMEC	breast:	n/a
27	chr4:2813458-2813508	NT2-D1	testis:	n/a
28	chr4:2813458-2813508	HEK293	kidney:	embryo
29	chr4:2813458-2813508	GM12878	blood:	n/a
30	chr4:2813458-2813508	MCF-7	breast:	n/a
31	chr4:2813458-2813508	SKMC	muscle:	n/a
32	chr4:2813458-2813508	ECC-1	luminal epithelium:	n/a
33	chr4:2813458-2813508	HAEpiC	amniotic membrane:	n/a
34	chr4:2813458-2813508	CMK	blood:	n/a
35	chr4:2813458-2813508	NHBE	bronchial:	n/a
36	chr4:2813458-2813508	HCM	heart:	n/a
37	chr4:2813458-2813508	U87	brain:	n/a
38	chr4:2813458-2813508	GM12892	blood:	n/a
39	chr4:2813458-2813508	HIPEpiC	eye:	n/a
40	chr4:2813458-2813508	Caco-2	colon:	n/a
41	chr4:2813458-2813508	BE2_C	brain:	n/a
42	chr4:2813458-2813508	MCF10A-Er-Src	breast:	n/a
43	chr4:2813458-2813508	PFSK-1	brain:	n/a
44	chr4:2813458-2813508	NB4	blood:	n/a
45	chr4:2813458-2813508	IMR90	lung:	fetal
46	chr4:2813458-2813508	HPAEpiC	pulmonary alveolar:	n/a
47	chr4:2813458-2813508	A549	lung:	n/a
48	chr4:2813458-2813508	HCF	heart:	n/a
49	chr4:2813458-2813508	HepG2	liver:	n/a
50	chr4:2813458-2813508	ovcar-3	ovarian:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:2812096..2814174-chr4:2819979..2821555,2	MCF-7	breast:
2	chr4:2812607..2814330-chr4:2927336..2930211,2	MCF-7	breast:

No data

Variant related genes	Relation type
SH3BP2	TF binding region
SH3BP2	CpG island
ENSG00000087266	Chromatin interaction
ENSG00000087274	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs13113803	0.81[ASN][1000 genomes]
rs13137906	0.90[ASN][1000 genomes]
rs1784148	0.91[ASN][1000 genomes]
rs1784149	0.91[ASN][1000 genomes]
rs2269484	0.82[ASN][1000 genomes]
rs2269485	0.90[ASN][1000 genomes]
rs2282770	0.90[ASN][1000 genomes]
rs2282771	0.90[ASN][1000 genomes]
rs3213501	0.91[ASN][1000 genomes]
rs34993433	0.91[ASN][1000 genomes]
rs370470	0.94[ASN][1000 genomes]
rs385715	0.87[ASN][1000 genomes]
rs393635	0.87[ASN][1000 genomes]
rs397292	0.90[ASN][1000 genomes]
rs402855	0.90[ASN][1000 genomes]
rs407770	0.90[ASN][1000 genomes]
rs419096	0.90[ASN][1000 genomes]
rs421714	0.97[ASN][1000 genomes]
rs422734	0.95[ASN][1000 genomes]
rs426904	0.97[ASN][1000 genomes]
rs433030	0.97[ASN][1000 genomes]
rs450080	0.96[ASN][1000 genomes]
rs6820967	0.97[ASN][1000 genomes]
rs9685721	0.91[ASN][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	nsv948659	chr4:1828867-2815632	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv878444	chr4:2689449-2861090	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv470002	chr4:2701098-2836628	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv878445	chr4:2704046-2831383	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv878447	chr4:2723531-2831383	Flanking Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv516797	chr4:2723531-2836628	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv878448	chr4:2723531-2846799	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	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
9	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
10	nsv878449	chr4:2744480-2831383	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv1002517	chr4:2747905-2822017	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Strong transcription 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	19 gene(s)	inside rSNPs	diseases
12	nsv878450	chr4:2760222-2861090	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	nsv593435	chr4:2770772-2881256	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv878451	chr4:2785556-2856687	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv878452	chr4:2789184-2830076	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv1010533	chr4:2792848-2873441	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv461162	chr4:2794320-2846799	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	nsv593436	chr4:2794320-2846799	Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2796200-2813800	Enhancers	Left Ventricle	heart
2	chr4:2796600-2814600	Enhancers	Stomach Mucosa	stomach
3	chr4:2803400-2819200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:2804600-2813800	Genic enhancers	Placenta	Placenta
5	chr4:2806000-2814600	Enhancers	Liver	Liver
6	chr4:2808400-2813800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:2809200-2815200	Weak transcription	Fetal Brain Female	brain
8	chr4:2810000-2813600	Enhancers	Primary B cells from peripheral blood	blood
9	chr4:2811000-2813600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:2811000-2813600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:2811000-2813600	Enhancers	Fetal Muscle Trunk	muscle
12	chr4:2811000-2813600	Enhancers	Lung	lung
13	chr4:2811000-2815200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:2811000-2816000	Enhancers	Brain Substantia Nigra	brain
15	chr4:2811200-2813600	Enhancers	Primary hematopoietic stem cells	blood
16	chr4:2811200-2813600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr4:2811200-2813800	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr4:2811200-2814000	Enhancers	Fetal Intestine Large	intestine
19	chr4:2811200-2814200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:2811200-2814600	Enhancers	Brain Anterior Caudate	brain
21	chr4:2811200-2814600	Genic enhancers	Fetal Intestine Small	intestine
22	chr4:2811200-2815000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:2811400-2814800	Enhancers	H1 Cell Line	embryonic stem cell
24	chr4:2811600-2813600	Enhancers	Brain Hippocampus Middle	brain
25	chr4:2811600-2815400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:2811800-2813600	Enhancers	Fetal Muscle Leg	muscle
27	chr4:2811800-2813800	Enhancers	Spleen	Spleen
28	chr4:2811800-2814400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:2811800-2815200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr4:2811800-2819400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:2812000-2813600	Enhancers	HepG2	liver
32	chr4:2812000-2815400	Weak transcription	Fetal Heart	heart
33	chr4:2812200-2813600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:2812200-2813600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr4:2812200-2815200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:2812400-2813600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr4:2812400-2813600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr4:2812400-2813800	Enhancers	Brain Cingulate Gyrus	brain
39	chr4:2812400-2813800	Enhancers	Fetal Thymus	thymus
40	chr4:2812400-2814000	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr4:2812400-2815200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr4:2812600-2813600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:2812600-2813600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:2812600-2815200	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr4:2812600-2815600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr4:2812800-2813600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:2812800-2813600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr4:2812800-2813600	Enhancers	Psoas Muscle	Psoas
49	chr4:2812800-2813600	Genic enhancers	Stomach Smooth Muscle	stomach
50	chr4:2812800-2815200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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