Variant report

Variant	rs4972396
Chromosome Location	chr2:173952932-173952933
allele	A/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	NR3C1	chr2:173952884-173953183	A549	lung:	n/a	n/a
2	CEBPB	chr2:173952729-173953382	A549	lung:	n/a	n/a
3	FOXA2	chr2:173952663-173953471	A549	lung:	n/a	n/a
4	GATA3	chr2:173952444-173953543	A549	lung:	n/a	n/a
5	FOXA1	chr2:173952801-173953327	HepG2	liver:	n/a	chr2:173953006-173953021 chr2:173953027-173953042
6	POLR2A	chr2:173952609-173953311	PANC-1	pancreas:	n/a	n/a
7	FOXA1	chr2:173952791-173953276	HepG2	liver:	n/a	chr2:173953006-173953021 chr2:173953027-173953042
8	TEAD4	chr2:173952920-173953404	A549	lung:	n/a	n/a
9	REST	chr2:173952818-173953157	A549	lung:	n/a	n/a
10	MAX	chr2:173952792-173953283	HepG2	liver:	n/a	n/a
11	FOXA2	chr2:173952523-173953915	HepG2	liver:	n/a	n/a
12	FOXA2	chr2:173952689-173953320	A549	lung:	n/a	n/a
13	REST	chr2:173952908-173953130	PANC-1	pancreas:	n/a	n/a
14	TCF7L2	chr2:173952636-173953204	PANC-1	pancreas:	n/a	n/a
15	FOXA2	chr2:173952827-173953202	HepG2	liver:	n/a	n/a
16	REST	chr2:173952805-173953195	HepG2	liver:	n/a	n/a
17	SP1	chr2:173952566-173953323	A549	lung:	n/a	n/a
18	FOXA1	chr2:173952847-173953257	HepG2	liver:	n/a	chr2:173953006-173953021 chr2:173953027-173953042
19	REST	chr2:173952694-173953284	PANC-1	pancreas:	n/a	n/a
20	REST	chr2:173952656-173953319	A549	lung:	n/a	n/a
21	SP1	chr2:173952519-173953455	A549	lung:	n/a	n/a
22	FOXA1	chr2:173952892-173953160	T-47D	breast:	n/a	chr2:173953006-173953021 chr2:173953027-173953042
23	TCF12	chr2:173952497-173953438	A549	lung:	n/a	n/a
24	TEAD4	chr2:173952805-173953316	A549	lung:	n/a	n/a
25	MAX	chr2:173952531-173953349	A549	lung:	n/a	n/a
26	CEBPB	chr2:173952822-173953264	A549	lung:	n/a	n/a
27	ARID3A	chr2:173952724-173953167	HepG2	liver:	n/a	n/a
28	FOXA1	chr2:173952806-173953205	HepG2	liver:	n/a	chr2:173953006-173953021 chr2:173953027-173953042
29	POLR2A	chr2:173952653-173953286	PANC-1	pancreas:	n/a	n/a
30	BCL3	chr2:173952730-173953395	A549	lung:	n/a	n/a
31	EP300	chr2:173952546-173953492	A549	lung:	n/a	n/a
32	NR3C1	chr2:173952886-173953254	A549	lung:	n/a	n/a
33	REST	chr2:173952808-173953309	PANC-1	pancreas:	n/a	n/a
34	NR3C1	chr2:173952832-173953158	A549	lung:	n/a	n/a
35	EP300	chr2:173952668-173953400	A549	lung:	n/a	n/a
36	FOXA1	chr2:173952819-173953164	T-47D	breast:	n/a	chr2:173953006-173953021 chr2:173953027-173953042
37	FOSL2	chr2:173952602-173953309	A549	lung:	n/a	n/a
38	MAX	chr2:173952722-173953327	A549	lung:	n/a	n/a
39	NR3C1	chr2:173952895-173953152	A549	lung:	n/a	n/a
40	GATA3	chr2:173952817-173953356	A549	lung:	n/a	n/a
41	GATA3	chr2:173952842-173953483	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:173950777..173953011-chr2:173954741..173957940,3	MCF-7	breast:
2	chr2:173951738..173953586-chr2:173954828..173957652,2	MCF-7	breast:
3	chr2:173944303..173947485-chr2:173950137..173953589,4	MCF-7	breast:
4	chr2:173951489..173953627-chr2:173981191..173983390,3	K562	blood:
5	chr2:173940052..173942648-chr2:173950228..173952997,4	MCF-7	breast:
6	chr2:173938088..173944133-chr2:173944779..173953152,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091436	TF binding region
ENSG00000091436	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10198781	0.85[AFR][1000 genomes]
rs11676760	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12693018	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13030567	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13031358	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13032024	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1345005	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1548045	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1866635	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2119125	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4146109	1.00[AMR][1000 genomes]
rs4972398	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4972537	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6433391	1.00[AMR][1000 genomes]
rs6433393	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6433394	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6433396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6433397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6713429	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6739869	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6741598	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173941600-173955200	Weak transcription	Lung	lung
2	chr2:173941600-173955200	Weak transcription	Pancreas	Pancrea
3	chr2:173941600-173969600	Weak transcription	Spleen	Spleen
4	chr2:173941800-173955200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:173941800-173955200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:173942000-173953000	Weak transcription	Stomach Mucosa	stomach
7	chr2:173942000-173955200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:173942000-173955400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:173942000-173956000	Weak transcription	Fetal Thymus	thymus
10	chr2:173942600-173956400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:173942800-173954800	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr2:173942800-173955800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr2:173942800-173964600	Weak transcription	HUVEC	blood vessel
14	chr2:173942800-173971400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:173943000-173971200	Weak transcription	HSMMtube	muscle
16	chr2:173943200-173955000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:173943400-173955200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:173943400-173955200	Weak transcription	Dnd41	blood
19	chr2:173943400-173974200	Weak transcription	Fetal Intestine Large	intestine
20	chr2:173943800-173956000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:173945400-173991200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:173947000-173955200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr2:173947400-173953200	Enhancers	Liver	Liver
24	chr2:173947600-173954200	Weak transcription	Fetal Intestine Small	intestine
25	chr2:173947600-173955000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:173947600-173955200	Weak transcription	Fetal Muscle Leg	muscle
27	chr2:173947600-173955200	Weak transcription	Gastric	stomach
28	chr2:173947600-173955200	Weak transcription	Right Atrium	heart
29	chr2:173948800-173955400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:173950400-173953800	Enhancers	Fetal Heart	heart
31	chr2:173951000-173953200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:173951000-173953200	Enhancers	Osteobl	bone
33	chr2:173951000-173953400	Enhancers	NHDF-Ad	bronchial
34	chr2:173951200-173953000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:173951200-173955000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:173951200-173955200	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr2:173951400-173957400	Weak transcription	Small Intestine	intestine
38	chr2:173951400-173962000	Weak transcription	Brain Substantia Nigra	brain
39	chr2:173951600-173955000	Weak transcription	Fetal Stomach	stomach
40	chr2:173951600-173955200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:173951600-173955200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:173951600-173955200	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr2:173951600-173955200	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr2:173951800-173953400	Enhancers	HepG2	liver
45	chr2:173951800-173954400	Weak transcription	K562	blood
46	chr2:173952000-173953000	Weak transcription	Fetal Lung	lung
47	chr2:173952000-173954000	Enhancers	NHLF	lung
48	chr2:173952000-173954800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr2:173952000-173955200	Weak transcription	Aorta	Aorta
50	chr2:173952000-173957600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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