Variant report

Variant	rs138540399
Chromosome Location	chr4:3342652-3342653
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:3342640-3342790	RPTEC	kidney:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
2	CTCF	chr4:3342617-3342799	MCF-7	breast:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
3	RAD21	chr4:3342587-3342869	HepG2	liver:	n/a	chr4:3342707-3342717 chr4:3342706-3342719 chr4:3342703-3342722 chr4:3342705-3342717
4	CTCF	chr4:3342524-3342842	T-47D	breast:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
5	CTCF	chr4:3342623-3342813	Pancreas_OC	pancreas:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
6	CTCF	chr4:3342520-3342670	HFF-Myc	foreskin:	n/a	n/a
7	CTCF	chr4:3342600-3342750	HRE	kidney:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
8	CTCF	chr4:3342491-3342790	T-47D	breast:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
9	CTCF	chr4:3342613-3342832	MCF-7	breast:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
10	RAD21	chr4:3342553-3342860	HepG2	liver:	n/a	chr4:3342707-3342717 chr4:3342706-3342719 chr4:3342703-3342722 chr4:3342705-3342717
11	CTCF	chr4:3342620-3342770	MCF-7	breast:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
12	CTCF	chr4:3342625-3342798	H1-hESC	embryonic stem cell:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
13	CTCF	chr4:3342620-3342770	A549	lung:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
14	CTCF	chr4:3342620-3342770	AG04450	lung:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
15	CTCF	chr4:3342600-3342750	GM06990	blood:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
16	CTCF	chr4:3342640-3342790	AG04449	skin:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
17	CTCF	chr4:3342588-3342875	MCF-7	breast:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
18	CTCF	chr4:3342610-3342834	NHEK	skin:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
19	RAD21	chr4:3342427-3342895	H1-hESC	embryonic stem cell:	n/a	chr4:3342707-3342717 chr4:3342706-3342719 chr4:3342431-3342445 chr4:3342703-3342722 chr4:3342705-3342717
20	CTCF	chr4:3342608-3342823	MCF-7	breast:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
21	RAD21	chr4:3342621-3342723	HepG2	liver:	n/a	chr4:3342707-3342717 chr4:3342706-3342719 chr4:3342703-3342722 chr4:3342705-3342717
22	CTCF	chr4:3342476-3342837	K562	blood:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
23	CTCF	chr4:3342620-3342770	SAEC	small airway:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
24	CTCF	chr4:3342640-3342790	HUVEC	blood vessel:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
25	HDAC2	chr4:3342628-3342874	K562	blood:	n/a	chr4:3342669-3342688
26	CTCF	chr4:3342645-3342751	Fibrobl	skin:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
27	CTCF	chr4:3342642-3342781	MCF-7	breast:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
28	CTCF	chr4:3342600-3342750	Hela-S3	cervix:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
29	CTCF	chr4:3342557-3342849	LNCaP	prostate:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
30	CTCF	chr4:3342542-3342802	K562	blood:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
31	SIN3A	chr4:3342611-3342675	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr4:3342620-3342770	HMEC	breast:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
33	CTCF	chr4:3342596-3342793	HepG2	liver:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
34	CTCF	chr4:3342577-3342854	LNCaP	prostate:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
35	CTCF	chr4:3342614-3342803	A549	lung:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
36	CTCF	chr4:3342640-3342790	WERI-Rb-1	eye:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
37	CTCF	chr4:3342640-3342790	HRE	kidney:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
38	CTCF	chr4:3342604-3342791	Lung_OC	lung:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
39	CTCF	chr4:3342628-3342781	Kidney_OC	kidney:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
40	CTCF	chr4:3342640-3342790	SAEC	small airway:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
41	CTCF	chr4:3342640-3342790	HEEpiC	esophagus:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
42	CTCF	chr4:3342580-3342730	HepG2	liver:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
43	CTCF	chr4:3342531-3342810	H1-hESC	embryonic stem cell:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
44	GATA3	chr4:3342620-3342797	T-47D	breast:	n/a	n/a
45	CTCF	chr4:3342632-3342797	GM12892	blood:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
46	CTCF	chr4:3342611-3342800	MCF-7	breast:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
47	RAD21	chr4:3342482-3342908	ECC-1	luminal epithelium:	n/a	chr4:3342707-3342717 chr4:3342706-3342719 chr4:3342703-3342722 chr4:3342705-3342717
48	CTCF	chr4:3342640-3342790	GM12870	blood:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
49	CTCF	chr4:3342605-3342747	K562	blood:	n/a	chr4:3342705-3342723 chr4:3342707-3342720
50	CTCF	chr4:3342566-3342873	GM12878	blood:	n/a	chr4:3342705-3342723 chr4:3342707-3342720

No.	Distal block	Cell Line	Cell type
1	chr4:3338818..3342772-chr4:3461368..3467187,7	MCF-7	breast:
2	chr4:3338889..3343165-chr4:3463099..3467145,4	MCF-7	breast:
3	chr4:3340754..3343218-chr4:3436055..3438880,2	MCF-7	breast:
4	chr4:3292758..3295748-chr4:3341243..3344299,3	MCF-7	breast:
5	chr4:3339354..3341969-chr4:3342389..3344050,2	MCF-7	breast:
6	chr4:3341846..3343634-chr4:3447069..3448712,2	MCF-7	breast:

Variant related genes	Relation type
RGS12	TF binding region
ENSG00000175920	Chromatin interaction
ENSG00000159788	Chromatin interaction
ENSG00000109758	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv878455	chr4:3215835-3344891	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
5	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS 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	33 gene(s)	inside rSNPs	diseases
7	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats 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	13 gene(s)	inside rSNPs	diseases
10	esv1803957	chr4:3339038-3343475	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	esv1837613	chr4:3339038-3343475	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	esv3398851	chr4:3341979-3344927	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv593443	chr4:3342137-3343418	Weak transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv593444	chr4:3342137-3343475	Weak transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv593445	chr4:3342137-3344891	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	nsv593446	chr4:3342137-3346617	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
17	esv3399978	chr4:3342179-3344577	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3301200-3350000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:3314400-3348200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:3320000-3344000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:3320400-3351800	Weak transcription	Aorta	Aorta
5	chr4:3321000-3347000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:3323600-3344000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:3323600-3344800	Weak transcription	Fetal Intestine Large	intestine
8	chr4:3324000-3343600	Weak transcription	HSMM	muscle
9	chr4:3324200-3343600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr4:3325200-3342800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr4:3325600-3348000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:3326200-3342800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:3326400-3343600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:3326400-3343600	Weak transcription	NHLF	lung
15	chr4:3326400-3343800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:3326400-3344800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:3326400-3348000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:3328400-3343600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:3330200-3343600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:3331000-3343600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr4:3332400-3343800	Weak transcription	Fetal Intestine Small	intestine
22	chr4:3332800-3343600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr4:3332800-3343600	Weak transcription	Primary T cells from cord blood	blood
24	chr4:3332800-3343600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:3334000-3345800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr4:3334000-3370600	Weak transcription	Right Atrium	heart
27	chr4:3334400-3343600	Weak transcription	Adipose Nuclei	Adipose
28	chr4:3334600-3343600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr4:3337000-3344000	Weak transcription	Fetal Kidney	kidney
30	chr4:3337400-3343600	Weak transcription	Ovary	ovary
31	chr4:3337400-3343600	Weak transcription	Right Ventricle	heart
32	chr4:3337600-3343600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:3338200-3343600	Weak transcription	Brain Anterior Caudate	brain
34	chr4:3338400-3343600	Weak transcription	HepG2	liver
35	chr4:3338400-3343800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr4:3339200-3353200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:3339800-3343600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:3339800-3343600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr4:3340200-3343200	Enhancers	Lung	lung
40	chr4:3340200-3344000	Enhancers	Brain Germinal Matrix	brain
41	chr4:3340400-3343600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:3340600-3343600	Weak transcription	Placenta	Placenta
43	chr4:3340800-3343600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:3340800-3344000	Enhancers	Fetal Brain Male	brain
45	chr4:3341000-3343000	Enhancers	Fetal Brain Female	brain
46	chr4:3341000-3343600	Weak transcription	HUVEC	blood vessel
47	chr4:3341200-3342800	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr4:3341200-3343600	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr4:3341200-3343600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr4:3341400-3342800	Enhancers	Esophagus	oesophagus

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