Variant report

Variant	rs1052595
Chromosome Location	chr4:779213-779214
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF2	chr4:779150-779350	H1-hESC	embryonic stem cell:	n/a	n/a
2	USF1	chr4:779050-779405	H1-hESC	embryonic stem cell:	n/a	n/a
3	POU5F1	chr4:779087-779551	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr4:778895-779391	H1-hESC	embryonic stem cell:	n/a	n/a
5	NANOG	chr4:779110-779563	H1-hESC	embryonic stem cell:	n/a	n/a
6	HDAC2	chr4:779097-779634	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F6	chr4:778798-779383	H1-hESC	embryonic stem cell:	n/a	n/a
8	GABPA	chr4:778731-779215	H1-hESC	embryonic stem cell:	n/a	n/a
9	SIN3A	chr4:778924-779458	H1-hESC	embryonic stem cell:	n/a	n/a
10	MXI1	chr4:779008-779312	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTBP2	chr4:779122-779556	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr4:778740-779461	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr4:779003-779312	K562	blood:	n/a	n/a
14	E2F6	chr4:778601-779529	H1-hESC	embryonic stem cell:	n/a	n/a
15	TCF12	chr4:779123-779480	H1-hESC	embryonic stem cell:	n/a	n/a
16	NANOG	chr4:779108-779389	H1-hESC	embryonic stem cell:	n/a	n/a
17	MYC	chr4:779034-779354	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr4:778731-779478	H1-hESC	embryonic stem cell:	n/a	n/a
19	USF1	chr4:779073-779401	H1-hESC	embryonic stem cell:	n/a	n/a
20	GTF2F1	chr4:779028-779265	H1-hESC	embryonic stem cell:	n/a	n/a
21	TCF12	chr4:779100-779589	H1-hESC	embryonic stem cell:	n/a	n/a
22	BACH1	chr4:778748-779581	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:779173-779223	LNCaP	prostate:	n/a
2	chr4:779173-779223	MCF-7	breast:	n/a
3	chr4:779173-779223	GM19239	blood:	n/a
4	chr4:779173-779223	NT2-D1	testis:	n/a
5	chr4:779173-779223	Jurkat	blood:	n/a
6	chr4:779173-779223	HepG2	liver:	n/a
7	chr4:779173-779223	K562	blood:	n/a
8	chr4:779173-779223	HCM	heart:	n/a
9	chr4:779173-779223	SKMC	muscle:	n/a
10	chr4:779173-779223	IMR90	lung:	fetal
11	chr4:779173-779223	AG09309	skin:	n/a
12	chr4:779173-779223	SK-N-MC	brain:	n/a
13	chr4:779173-779223	PrEC	prostate:	n/a
14	chr4:779173-779223	NB4	blood:	n/a
15	chr4:779173-779223	MCF10A-Er-Src	breast:	n/a
16	chr4:779173-779223	ProgFib	skin:	n/a
17	chr4:779173-779223	SK-N-SH	brain:	n/a
18	chr4:779173-779223	HCT-116	colon:	n/a
19	chr4:779173-779223	ovcar-3	ovarian:	n/a
20	chr4:779173-779223	AG09319	gingival:	n/a
21	chr4:779173-779223	CMK	blood:	n/a
22	chr4:779173-779223	HEK293	kidney:	embryo
23	chr4:779173-779223	Caco-2	colon:	n/a
24	chr4:779173-779223	SAEC	small airway:	n/a
25	chr4:779173-779223	NHDF-neo	bronchial:	n/a
26	chr4:779173-779223	HCPEpiC	choroid plexus:	n/a
27	chr4:779173-779223	PFSK-1	brain:	n/a
28	chr4:779173-779223	GM12891	blood:	n/a
29	chr4:779173-779223	HNPCEpiC	eye:	n/a
30	chr4:779173-779223	BE2_C	brain:	n/a
31	chr4:779173-779223	AG04450	lung:	fetal
32	chr4:779173-779223	Hepatocyte	liver:	n/a
33	chr4:779173-779223	GM06990	blood:	n/a
34	chr4:779173-779223	HUVEC	blood vessel:	n/a
35	chr4:779173-779223	HRCEpiC	kidney:	n/a
36	chr4:779173-779223	HEEpiC	esophagus:	n/a
37	chr4:779173-779223	NHBE	bronchial:	n/a
38	chr4:779173-779223	PANC-1	pancreas:	n/a
39	chr4:779173-779223	SK-N-SH_RA	brain:	n/a
40	chr4:779173-779223	H1-hESC	embryonic stem cell:	embryo
41	chr4:779173-779223	AG10803	skin:	n/a
42	chr4:779173-779223	HPAEpiC	pulmonary alveolar:	n/a
43	chr4:779173-779223	HCF	heart:	n/a
44	chr4:779173-779223	T-47D	breast:	n/a
45	chr4:779173-779223	Hela-S3	cervix:	n/a
46	chr4:779173-779223	HAEpiC	amniotic membrane:	n/a
47	chr4:779173-779223	AoSMC	blood vessel:	n/a
48	chr4:779173-779223	HRPEpiC	eye:	n/a
49	chr4:779173-779223	NH-A	brain:	n/a
50	chr4:779173-779223	RPTEC	kidney:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:779184..781836-chr4:815756..818416,2	MCF-7	breast:
2	chr4:675173..676793-chr4:777348..779688,2	MCF-7	breast:
3	chr4:776936..779756-chr4:805592..808402,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000249592	TF binding region
ENSG00000249592	CpG island

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2242236	0.91[ASN][1000 genomes]
rs2306251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6810428	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats 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	76 gene(s)	inside rSNPs	diseases
2	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	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
5	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription 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
8	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
9	esv1829397	chr4:655939-1041957	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
10	nsv878254	chr4:708932-899143	Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv878255	chr4:708932-1052488	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
12	nsv878257	chr4:712222-852313	Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv878258	chr4:712222-1058358	Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
14	nsv878259	chr4:713920-852313	Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv878260	chr4:713920-1052488	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
16	nsv818207	chr4:753944-821490	Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
17	nsv878261	chr4:756686-1047794	Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats 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
18	nsv1007928	chr4:757263-813885	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
19	nsv520136	chr4:759709-780883	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
20	nsv1003219	chr4:769894-1105464	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
21	nsv515844	chr4:771587-780883	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
22	nsv526780	chr4:771587-786401	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
23	nsv521402	chr4:771587-793763	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
24	nsv878262	chr4:771587-865227	Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
25	nsv878263	chr4:771587-1047794	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
26	nsv964736	chr4:777089-807477	Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:776400-779400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr4:777400-780000	Weak transcription	Pancreas	Pancrea
3	chr4:777400-780800	Weak transcription	GM12878-XiMat	blood
4	chr4:777800-781800	Weak transcription	Liver	Liver
5	chr4:778000-779400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:778200-779600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:778200-780200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr4:778200-780200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
9	chr4:778400-780600	Bivalent Enhancer	Spleen	Spleen
10	chr4:778400-780800	Bivalent Enhancer	Fetal Brain Male	brain
11	chr4:778400-781200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
12	chr4:778600-779400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
13	chr4:778600-779400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
14	chr4:778600-779800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
15	chr4:778600-780400	Bivalent Enhancer	Fetal Intestine Small	intestine
16	chr4:778600-780800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
17	chr4:778600-784800	Bivalent Enhancer	Fetal Thymus	thymus
18	chr4:778800-779400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
19	chr4:778800-779400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:778800-779400	Bivalent Enhancer	Colonic Mucosa	Colon
21	chr4:778800-779400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
22	chr4:778800-779600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
23	chr4:778800-779600	Bivalent Enhancer	Brain Hippocampus Middle	brain
24	chr4:778800-779600	Bivalent Enhancer	Fetal Lung	lung
25	chr4:778800-779600	Bivalent Enhancer	Fetal Muscle Leg	muscle
26	chr4:778800-779600	Enhancers	Gastric	stomach
27	chr4:778800-779800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:778800-779800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr4:778800-779800	Bivalent Enhancer	Brain Substantia Nigra	brain
30	chr4:778800-779800	Bivalent Enhancer	Placenta	Placenta
31	chr4:778800-780000	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:778800-780000	Enhancers	Lung	lung
33	chr4:778800-780600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:778800-780600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr4:778800-780600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
36	chr4:778800-781400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:779000-779400	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr4:779000-779400	Bivalent Enhancer	Primary B cells from cord blood	blood
39	chr4:779000-779400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
40	chr4:779000-779400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
41	chr4:779000-779400	Bivalent Enhancer	Fetal Heart	heart
42	chr4:779000-779400	Bivalent Enhancer	Fetal Stomach	stomach
43	chr4:779000-779400	Enhancers	Right Atrium	heart
44	chr4:779000-779600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr4:779000-779600	Bivalent Enhancer	Fetal Intestine Large	intestine
46	chr4:779000-779600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
47	chr4:779000-779600	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
48	chr4:779000-779600	Flanking Active TSS	Right Ventricle	heart
49	chr4:779000-779800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
50	chr4:779000-780000	Bivalent Enhancer	Primary hematopoietic stem cells	blood

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