Variant report

Variant	rs13106867
Chromosome Location	chr4:2941317-2941318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:55)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:55 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:2941224-2941480	Hela-S3	cervix:	n/a	n/a
2	JUND	chr4:2941277-2941527	HepG2	liver:	n/a	chr4:2941400-2941411 chr4:2941402-2941409 chr4:2941401-2941410 chr4:2941401-2941411 chr4:2941402-2941411
3	POLR2A	chr4:2940384-2943197	K562	blood:	n/a	n/a
4	POLR2A	chr4:2940251-2945411	MCF-7	breast:	n/a	n/a
5	POLR2A	chr4:2940550-2945810	K562	blood:	n/a	n/a
6	POLR2A	chr4:2941232-2941526	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr4:2941042-2941550	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr4:2940406-2943625	K562	blood:	n/a	n/a
9	POLR2A	chr4:2941092-2941921	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr4:2940443-2946234	GM12892	blood:	n/a	n/a
11	POLR2A	chr4:2940559-2945452	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr4:2940564-2945754	HL-60	blood:	n/a	n/a
13	POLR2A	chr4:2940541-2945723	GM12892	blood:	n/a	n/a
14	POLR2A	chr4:2940785-2943731	HepG2	liver:	n/a	n/a
15	POLR2A	chr4:2940925-2945690	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:2940667-2945696	K562	blood:	n/a	n/a
17	POLR2A	chr4:2940712-2943487	NB4	blood:	n/a	n/a
18	POLR2A	chr4:2940210-2942150	K562	blood:	n/a	n/a
19	POLR2A	chr4:2936437-2945444	GM12892	blood:	n/a	n/a
20	POLR2A	chr4:2941017-2943702	GM12878	blood:	n/a	n/a
21	POLR2A	chr4:2940661-2944919	K562	blood:	n/a	n/a
22	POLR2A	chr4:2940303-2945445	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr4:2940538-2945308	GM12891	blood:	n/a	n/a
24	POLR2A	chr4:2940865-2941355	U87	brain:	n/a	n/a
25	POLR2A	chr4:2940169-2946206	GM12892	blood:	n/a	n/a
26	POLR2A	chr4:2940421-2946090	GM18505	blood:	n/a	n/a
27	POLR2A	chr4:2941043-2941925	GM12878	blood:	n/a	n/a
28	POLR2A	chr4:2940394-2946126	GM12878	blood:	n/a	n/a
29	POLR2A	chr4:2940578-2945412	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr4:2941247-2943491	HEK293	kidney:	n/a	n/a
31	POLR2A	chr4:2940727-2941980	HepG2	liver:	n/a	n/a
32	POLR2A	chr4:2941064-2945424	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr4:2936414-2946052	SK-N-MC	brain:	n/a	n/a
34	POLR2A	chr4:2940213-2943154	K562	blood:	n/a	n/a
35	POLR2A	chr4:2940245-2946157	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr4:2940527-2945354	GM12891	blood:	n/a	n/a
37	POLR2A	chr4:2940108-2945313	HL-60	blood:	n/a	n/a
38	POLR2A	chr4:2940267-2946154	K562	blood:	n/a	n/a
39	POLR2A	chr4:2940134-2945737	GM12878	blood:	n/a	n/a
40	POLR2A	chr4:2940722-2946089	GM19193	blood:	n/a	n/a
41	POLR2A	chr4:2940408-2945724	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr4:2940553-2945342	GM12891	blood:	n/a	n/a
43	POLR2A	chr4:2940696-2945531	PANC-1	pancreas:	n/a	n/a
44	POLR2A	chr4:2940222-2945187	PFSK-1	brain:	n/a	n/a
45	POLR2A	chr4:2940145-2941975	GM12878	blood:	n/a	n/a
46	RUNX3	chr4:2941266-2941532	GM12878	blood:	n/a	n/a
47	POLR2A	chr4:2940867-2941605	GM12891	blood:	n/a	n/a
48	POLR2A	chr4:2940343-2946084	GM12891	blood:	n/a	n/a
49	FOS	chr4:2941278-2941510	MCF10A-Er-Src	breast:	n/a	chr4:2941402-2941409 chr4:2941401-2941410 chr4:2941401-2941411 chr4:2941402-2941411
50	POLR2A	chr4:2940899-2941338	U87	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:2941316-2941366	AG09309	skin:	n/a
2	chr4:2941316-2941366	K562	blood:	n/a
3	chr4:2941316-2941366	HMEC	breast:	n/a
4	chr4:2941316-2941366	PrEC	prostate:	n/a
5	chr4:2941316-2941366	HEEpiC	esophagus:	n/a
6	chr4:2941316-2941366	SK-N-SH_RA	brain:	n/a
7	chr4:2941316-2941366	AoSMC	blood vessel:	n/a
8	chr4:2941316-2941366	HRE	kidney:	n/a
9	chr4:2941316-2941366	NH-A	brain:	n/a
10	chr4:2941316-2941366	HCT-116	colon:	n/a
11	chr4:2941316-2941366	HRPEpiC	eye:	n/a
12	chr4:2941316-2941366	PANC-1	pancreas:	n/a
13	chr4:2941316-2941366	Hepatocyte	liver:	n/a
14	chr4:2941316-2941366	HEK293	kidney:	embryo
15	chr4:2941316-2941366	ECC-1	luminal epithelium:	n/a
16	chr4:2941316-2941366	NT2-D1	testis:	n/a
17	chr4:2941316-2941366	BE2_C	brain:	n/a
18	chr4:2941316-2941366	HPAEpiC	pulmonary alveolar:	n/a
19	chr4:2941316-2941366	GM12878	blood:	n/a
20	chr4:2941316-2941366	HIPEpiC	eye:	n/a
21	chr4:2941316-2941366	AG04450	lung:	fetal
22	chr4:2941316-2941366	LNCaP	prostate:	n/a
23	chr4:2941316-2941366	GM12891	blood:	n/a
24	chr4:2941316-2941366	T-47D	breast:	n/a
25	chr4:2941316-2941366	HCF	heart:	n/a
26	chr4:2941316-2941366	GM12892	blood:	n/a
27	chr4:2941316-2941366	GM06990	blood:	n/a
28	chr4:2941316-2941366	NB4	blood:	n/a
29	chr4:2941316-2941366	BJ	skin:	n/a
30	chr4:2941316-2941366	AG10803	skin:	n/a
31	chr4:2941316-2941366	SK-N-MC	brain:	n/a
32	chr4:2941316-2941366	CMK	blood:	n/a
33	chr4:2941316-2941366	AG04449	skin:	fetal
34	chr4:2941316-2941366	H1-hESC	embryonic stem cell:	embryo
35	chr4:2941316-2941366	Jurkat	blood:	n/a
36	chr4:2941316-2941366	A549	lung:	n/a
37	chr4:2941316-2941366	SKMC	muscle:	n/a
38	chr4:2941316-2941366	HCPEpiC	choroid plexus:	n/a
39	chr4:2941316-2941366	NHBE	bronchial:	n/a
40	chr4:2941316-2941366	MCF10A-Er-Src	breast:	n/a
41	chr4:2941316-2941366	ovcar-3	ovarian:	n/a
42	chr4:2941316-2941366	HepG2	liver:	n/a
43	chr4:2941316-2941366	SAEC	small airway:	n/a
44	chr4:2941316-2941366	HAEpiC	amniotic membrane:	n/a
45	chr4:2941316-2941366	AG09319	gingival:	n/a
46	chr4:2941316-2941366	GM19239	blood:	n/a
47	chr4:2941316-2941366	MCF-7	breast:	n/a
48	chr4:2941316-2941366	SK-N-SH	brain:	n/a
49	chr4:2941316-2941366	Hela-S3	cervix:	n/a
50	chr4:2941316-2941366	HRCEpiC	kidney:	n/a

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:2744882..2747372-chr4:2939204..2941468,2	MCF-7	breast:
2	chr4:2903718..2915473-chr4:2930612..2941584,27	MCF-7	breast:
3	chr4:2790052..2809152-chr4:2930639..2948075,83	MCF-7	breast:
4	chr4:2941284..2943346-chr4:2963790..2966270,3	MCF-7	breast:
5	chr4:2940357..2942863-chr4:2954214..2956464,2	K562	blood:
6	chr4:2798770..2801758-chr4:2941180..2943976,2	K562	blood:
7	chr17:700252..700898-chr4:2940705..2941671,2	Hela-S3	cervix:
8	chr4:2753882..2759883-chr4:2932429..2941474,15	MCF-7	breast:
9	chr4:2906552..2911481-chr4:2934891..2942965,11	MCF-7	breast:
10	chr4:2844829..2846512-chr4:2941018..2943974,2	K562	blood:

No data

Variant related genes	Relation type
MFSD10	TF binding region
MFSD10	CpG island
ENSG00000087274	Chromatin interaction
ENSG00000168884	Chromatin interaction
ENSG00000087266	Chromatin interaction
ENSG00000087269	Chromatin interaction
ENSG00000125388	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1034400	1.00[CHD][hapmap]
rs16843503	1.00[MKK][hapmap]
rs2295497	1.00[LWK][hapmap]
rs2858039	1.00[LWK][hapmap]
rs3213502	1.00[LWK][hapmap]
rs35037838	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35916613	1.00[EUR][1000 genomes]
rs3733220	1.00[CHD][hapmap]
rs4690006	1.00[CHB][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription 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	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2937800-2941800	Weak transcription	Small Intestine	intestine
2	chr4:2937800-2942400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:2937800-2945800	Weak transcription	Fetal Kidney	kidney
4	chr4:2938000-2945400	Genic enhancers	Primary T cells fromperipheralblood	blood
5	chr4:2938000-2960400	Weak transcription	Right Atrium	heart
6	chr4:2938200-2946800	Strong transcription	Thymus	Thymus
7	chr4:2938200-2948400	Strong transcription	Fetal Intestine Small	intestine
8	chr4:2938200-2962200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:2938400-2944400	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:2938400-2957600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr4:2938400-2959600	Strong transcription	Brain Anterior Caudate	brain
12	chr4:2938400-2962200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:2938600-2943800	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr4:2938600-2949600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:2938600-2960400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:2938600-2960400	Strong transcription	Brain Cingulate Gyrus	brain
17	chr4:2938600-2961000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr4:2938600-2961600	Strong transcription	Primary T cells from cord blood	blood
19	chr4:2938600-2961600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:2938800-2944000	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr4:2938800-2955600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:2938800-2956800	Strong transcription	Fetal Intestine Large	intestine
23	chr4:2938800-2959200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:2938800-2961000	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr4:2938800-2961000	Strong transcription	Primary hematopoietic stem cells	blood
26	chr4:2938800-2961000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:2939000-2943000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:2939000-2956800	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr4:2939000-2956800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:2939000-2957400	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr4:2939000-2958400	Strong transcription	Brain Substantia Nigra	brain
32	chr4:2939000-2960200	Strong transcription	Lung	lung
33	chr4:2939000-2961600	Strong transcription	Fetal Stomach	stomach
34	chr4:2939200-2953800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:2939200-2956200	Strong transcription	Left Ventricle	heart
36	chr4:2939200-2959200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:2939200-2959600	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr4:2939200-2960000	Strong transcription	Stomach Smooth Muscle	stomach
39	chr4:2939200-2960600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr4:2939200-2961000	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr4:2939200-2963200	Weak transcription	Fetal Heart	heart
42	chr4:2939400-2941400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:2939400-2942600	Strong transcription	Esophagus	oesophagus
44	chr4:2939400-2944200	Strong transcription	Duodenum Mucosa	Duodenum
45	chr4:2939400-2945800	Strong transcription	HSMMtube	muscle
46	chr4:2939400-2948000	Strong transcription	Liver	Liver
47	chr4:2939400-2952600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:2939400-2956800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:2939400-2957200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:2939400-2959000	Strong transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links