Variant report

Variant	rs2716723
Chromosome Location	chr2:39924139-39924140
allele	A/T
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	RAD21	chr2:39923977-39924386	Hela-S3	cervix:	n/a	chr2:39924087-39924106
2	RAD21	chr2:39923183-39924750	SK-N-SH	brain:	n/a	chr2:39924087-39924106
3	JUN	chr2:39923916-39924326	HUVEC	blood vessel:	n/a	n/a
4	CTCF	chr2:39924100-39924250	BJ	skin:	n/a	chr2:39924214-39924235
5	CTCF	chr2:39924120-39924270	AG04449	skin:	n/a	chr2:39924214-39924235
6	CTCF	chr2:39924120-39924270	HMEC	breast:	n/a	chr2:39924214-39924235
7	CTCF	chr2:39924120-39924270	HUVEC	blood vessel:	n/a	chr2:39924214-39924235
8	CTCF	chr2:39924100-39924250	GM06990	blood:	n/a	chr2:39924214-39924235
9	RAD21	chr2:39923904-39924482	ECC-1	luminal epithelium:	n/a	chr2:39924087-39924106
10	RAD21	chr2:39924087-39924371	HepG2	liver:	n/a	chr2:39924087-39924106
11	SMC3	chr2:39924092-39924315	HepG2	liver:	n/a	n/a
12	CTCF	chr2:39923779-39924598	A549	lung:	n/a	chr2:39924092-39924102 chr2:39924084-39924105 chr2:39924214-39924235
13	CTCF	chr2:39924124-39924165	Gliobla	brain:	n/a	n/a
14	CTCF	chr2:39924100-39924250	HPAF	blood vessel:	n/a	chr2:39924214-39924235
15	RAD21	chr2:39923972-39924499	MCF-7	breast:	n/a	chr2:39924087-39924106
16	CTCF	chr2:39924080-39924230	HPF	lung:	n/a	chr2:39924092-39924102 chr2:39924084-39924105
17	STAT3	chr2:39923994-39924356	MCF10A-Er-Src	breast:	n/a	n/a
18	RAD21	chr2:39924087-39924304	H1-hESC	embryonic stem cell:	n/a	chr2:39924087-39924106
19	SMC3	chr2:39924067-39924306	K562	blood:	n/a	chr2:39924091-39924105
20	CTCF	chr2:39924020-39924170	BE2_C	brain:	n/a	chr2:39924092-39924102 chr2:39924084-39924105
21	CTCF	chr2:39923996-39924395	A549	lung:	n/a	chr2:39924092-39924102 chr2:39924084-39924105 chr2:39924214-39924235
22	CTCF	chr2:39924100-39924250	SAEC	small airway:	n/a	chr2:39924214-39924235
23	RAD21	chr2:39923914-39924533	A549	lung:	n/a	chr2:39924087-39924106
24	CTCF	chr2:39923936-39924450	HCT-116	colon:	n/a	chr2:39924092-39924102 chr2:39924084-39924105 chr2:39924214-39924235
25	CTCF	chr2:39924120-39924270	BE2_C	brain:	n/a	chr2:39924214-39924235
26	CTCF	chr2:39924100-39924250	HEEpiC	esophagus:	n/a	chr2:39924214-39924235
27	CTCF	chr2:39923779-39924694	SK-N-SH	brain:	n/a	chr2:39924092-39924102 chr2:39924084-39924105 chr2:39924214-39924235
28	CTCF	chr2:39924120-39924270	BJ	skin:	n/a	chr2:39924214-39924235
29	RAD21	chr2:39923912-39924374	SK-N-SH_RA	brain:	n/a	chr2:39924087-39924106
30	RAD21	chr2:39924072-39924354	A549	lung:	n/a	chr2:39924087-39924106
31	RAD21	chr2:39923994-39924450	HepG2	liver:	n/a	chr2:39924087-39924106
32	FOXM1	chr2:39922976-39924402	ECC-1	luminal epithelium:	n/a	n/a
33	CTCF	chr2:39924020-39924170	HCM	heart:	n/a	chr2:39924092-39924102 chr2:39924084-39924105
34	CTCF	chr2:39924020-39924170	AG04450	lung:	n/a	chr2:39924092-39924102 chr2:39924084-39924105
35	CTCF	chr2:39924139-39924313	Spleen_OC	spleen:	n/a	chr2:39924214-39924235
36	CTCF	chr2:39924001-39924318	A549	lung:	n/a	chr2:39924092-39924102 chr2:39924084-39924105 chr2:39924214-39924235
37	EP300	chr2:39922925-39924146	ECC-1	luminal epithelium:	n/a	n/a
38	CTCF	chr2:39924100-39924250	HL-60	blood:	n/a	chr2:39924214-39924235
39	CTCF	chr2:39924100-39924250	HUVEC	blood vessel:	n/a	chr2:39924214-39924235
40	SMC3	chr2:39923971-39924357	Hela-S3	cervix:	n/a	chr2:39924091-39924105
41	CTCF	chr2:39924070-39924365	GM12878	blood:	n/a	chr2:39924092-39924102 chr2:39924084-39924105 chr2:39924214-39924235
42	RAD21	chr2:39923961-39924678	IMR90	lung:	n/a	chr2:39924087-39924106
43	CTCF	chr2:39924001-39924454	MCF-7	breast:	n/a	chr2:39924092-39924102 chr2:39924084-39924105 chr2:39924214-39924235
44	CTCF	chr2:39924107-39924303	Medullo	brain:	n/a	chr2:39924214-39924235
45	CTCF	chr2:39924120-39924270	HCPEpiC	choroid plexus:	n/a	chr2:39924214-39924235
46	CTCF	chr2:39924120-39924270	NHDF-neo	bronchial:	n/a	chr2:39924214-39924235
47	CTCF	chr2:39924100-39924250	MCF-7	breast:	n/a	chr2:39924214-39924235
48	CTCF	chr2:39924120-39924270	HBMEC	blood vessel:	n/a	chr2:39924214-39924235
49	CTCF	chr2:39924120-39924270	HCM	heart:	n/a	chr2:39924214-39924235
50	SMC3	chr2:39922931-39924711	SK-N-SH	brain:	n/a	chr2:39924091-39924105

No.	Distal block	Cell Line	Cell type
1	chr2:39924084..39924628-chr2:39955735..39956340,2	MCF-7	breast:
2	chr2:39820776..39821515-chr2:39923747..39924593,3	MCF-7	breast:
3	chr2:39743453..39744065-chr2:39923644..39924443,2	MCF-7	breast:
4	chr2:39820592..39821545-chr2:39923733..39924738,7	MCF-7	breast:
5	chr2:39740456..39741440-chr2:39923994..39925288,5	MCF-7	breast:

Variant related genes	Relation type
TMEM178A	TF binding region
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs17024242	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2540230	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2540231	1.00[AMR][1000 genomes]
rs2540232	1.00[AMR][1000 genomes]
rs2540237	1.00[AMR][1000 genomes]
rs2540238	0.85[AFR][1000 genomes]
rs2540239	0.85[AFR][1000 genomes]
rs2540240	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2540246	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716680	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716689	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716695	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs2716696	0.80[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716708	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716710	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716725	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716728	1.00[AMR][1000 genomes]
rs2716731	1.00[AMR][1000 genomes]
rs57481251	1.00[AMR][1000 genomes]
rs6746083	1.00[AMR][1000 genomes]
rs73924911	1.00[AMR][1000 genomes]
rs73924912	1.00[AMR][1000 genomes]
rs73924913	1.00[AMR][1000 genomes]
rs73924914	1.00[AMR][1000 genomes]
rs73924935	1.00[AMR][1000 genomes]
rs73924936	1.00[AMR][1000 genomes]
rs7559933	1.00[AMR][1000 genomes]
rs917968	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873889	chr2:39830183-39950482	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39914200-39926800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:39921400-39924800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:39921600-39925200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr2:39921600-39925200	Enhancers	Brain Cingulate Gyrus	brain
5	chr2:39922000-39924200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:39922000-39924800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:39922000-39925200	Enhancers	HSMMtube	muscle
8	chr2:39922200-39924200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:39922200-39925000	Enhancers	Fetal Stomach	stomach
10	chr2:39922200-39925200	Enhancers	Fetal Lung	lung
11	chr2:39922400-39925200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr2:39922400-39925200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr2:39922600-39924200	Enhancers	NHLF	lung
14	chr2:39922600-39925000	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr2:39922600-39925200	Enhancers	Brain Angular Gyrus	brain
16	chr2:39922800-39924200	Enhancers	Muscle Satellite Cultured Cells	--
17	chr2:39922800-39925200	Enhancers	Psoas Muscle	Psoas
18	chr2:39923000-39924600	Weak transcription	Right Atrium	heart
19	chr2:39923000-39925200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:39923200-39924200	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr2:39923200-39924800	Enhancers	HUVEC	blood vessel
22	chr2:39923200-39925000	Enhancers	Brain Substantia Nigra	brain
23	chr2:39923200-39925200	Enhancers	Brain Anterior Caudate	brain
24	chr2:39923200-39925200	Enhancers	Colon Smooth Muscle	Colon
25	chr2:39923200-39925600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:39923400-39924200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr2:39923400-39924200	Enhancers	Fetal Kidney	kidney
28	chr2:39923400-39924600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr2:39923400-39924800	Enhancers	Adipose Nuclei	Adipose
30	chr2:39923400-39924800	Enhancers	Osteobl	bone
31	chr2:39923400-39925000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:39923400-39925000	Enhancers	Rectal Smooth Muscle	rectum
33	chr2:39923400-39925200	Enhancers	Fetal Brain Male	brain
34	chr2:39923400-39925400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:39923400-39925600	Enhancers	Fetal Brain Female	brain
36	chr2:39923600-39924600	Weak transcription	Lung	lung
37	chr2:39923600-39926200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:39923600-39935200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:39923800-39924400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr2:39923800-39924800	Weak transcription	Left Ventricle	heart
41	chr2:39923800-39925200	Enhancers	HMEC	breast
42	chr2:39923800-39925200	Enhancers	HSMM	muscle
43	chr2:39924000-39924200	Flanking Active TSS	Fetal Heart	heart
44	chr2:39924000-39924400	Active TSS	Brain Hippocampus Middle	brain
45	chr2:39924000-39924400	Weak transcription	Fetal Muscle Leg	muscle
46	chr2:39924000-39925000	Weak transcription	NH-A	brain

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