Variant report

Variant	rs72820411
Chromosome Location	chr2:48571851-48571852
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	KAP1	chr2:48570881-48571860	HEK293	kidney:	n/a	chr2:48571522-48571531
2	TCF12	chr2:48570813-48571987	SK-N-SH	brain:	n/a	n/a
3	FOXA2	chr2:48571278-48571870	A549	lung:	n/a	chr2:48571350-48571362
4	TCF12	chr2:48570574-48572155	A549	lung:	n/a	n/a
5	MBD4	chr2:48571113-48571997	HepG2	liver:	n/a	n/a
6	GATA3	chr2:48570616-48572011	SK-N-SH	brain:	n/a	chr2:48571468-48571478 chr2:48571468-48571475 chr2:48571467-48571475 chr2:48571463-48571479 chr2:48571466-48571476 chr2:48571461-48571482 chr2:48571468-48571475 chr2:48571468-48571475 chr2:48571415-48571425
7	RXRA	chr2:48571189-48571886	SK-N-SH	brain:	n/a	chr2:48571521-48571530
8	NFIC	chr2:48571032-48571925	SK-N-SH	brain:	n/a	n/a
9	GATA3	chr2:48570698-48571959	SK-N-SH	brain:	n/a	chr2:48571468-48571478 chr2:48571468-48571475 chr2:48571467-48571475 chr2:48571463-48571479 chr2:48571466-48571476 chr2:48571461-48571482 chr2:48571468-48571475 chr2:48571468-48571475 chr2:48571415-48571425
10	JUND	chr2:48571099-48571865	SK-N-SH	brain:	n/a	chr2:48571521-48571529 chr2:48571522-48571529
11	FOXA2	chr2:48570899-48573824	HepG2	liver:	n/a	chr2:48571194-48571206 chr2:48571350-48571362
12	PBX3	chr2:48571125-48571889	SK-N-SH	brain:	n/a	n/a
13	EP300	chr2:48571023-48571948	SK-N-SH	brain:	n/a	chr2:48571121-48571135 chr2:48571896-48571910
14	TEAD4	chr2:48571091-48571869	SK-N-SH	brain:	n/a	n/a
15	TEAD4	chr2:48571094-48571909	SK-N-SH	brain:	n/a	n/a
16	JUND	chr2:48571106-48571879	SK-N-SH	brain:	n/a	chr2:48571521-48571529 chr2:48571522-48571529
17	STAT3	chr2:48571378-48571891	MCF10A-Er-Src	breast:	n/a	chr2:48571385-48571396
18	TCF12	chr2:48570853-48571944	SK-N-SH	brain:	n/a	n/a
19	GATA3	chr2:48570808-48571971	A549	lung:	n/a	chr2:48571468-48571478 chr2:48571468-48571475 chr2:48571467-48571475 chr2:48571463-48571479 chr2:48571466-48571476 chr2:48571461-48571482 chr2:48571468-48571475 chr2:48571468-48571475 chr2:48571415-48571425
20	MAX	chr2:48571270-48571894	A549	lung:	n/a	n/a
21	MXI1	chr2:48571157-48571871	Hela-S3	cervix:	n/a	n/a
22	SIN3AK20	chr2:48571035-48571901	MCF-7	breast:	n/a	n/a
23	NFIC	chr2:48571166-48571864	HepG2	liver:	n/a	n/a
24	EP300	chr2:48571017-48571935	SK-N-SH	brain:	n/a	chr2:48571121-48571135 chr2:48571896-48571910
25	FOSL2	chr2:48570939-48571898	A549	lung:	n/a	chr2:48571521-48571529 chr2:48571522-48571529
26	PBX3	chr2:48570883-48571928	SK-N-SH	brain:	n/a	n/a
27	TEAD4	chr2:48571174-48572885	HepG2	liver:	n/a	n/a
28	ARID3A	chr2:48570947-48571931	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48541369..48544104-chr2:48569607..48573166,3	MCF-7	breast:
2	chr2:48566382..48569170-chr2:48571400..48573761,2	K562	blood:

Variant related genes	Relation type
RNU4-49P	TF binding region
ENSG00000251889	Chromatin interaction
ENSG00000170802	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10169629	0.90[ASN][1000 genomes]
rs10208627	0.82[ASN][1000 genomes]
rs10495951	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10495952	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11676036	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11679523	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11680916	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11682633	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11683099	0.90[ASN][1000 genomes]
rs11684517	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11685861	0.95[ASN][1000 genomes]
rs11686007	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11687708	0.85[ASN][1000 genomes]
rs11688481	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11689645	0.88[ASN][1000 genomes]
rs11690690	0.94[ASN][1000 genomes]
rs11690748	0.95[ASN][1000 genomes]
rs11690845	0.94[ASN][1000 genomes]
rs12052754	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12105983	0.82[ASN][1000 genomes]
rs12328506	0.90[ASN][1000 genomes]
rs13398791	0.90[ASN][1000 genomes]
rs17037289	0.92[ASN][1000 genomes]
rs17037298	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17855177	0.94[ASN][1000 genomes]
rs4344965	0.94[ASN][1000 genomes]
rs4547570	0.90[ASN][1000 genomes]
rs55660911	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55744465	0.88[ASN][1000 genomes]
rs55761545	0.94[ASN][1000 genomes]
rs55788229	0.84[ASN][1000 genomes]
rs56156294	0.88[ASN][1000 genomes]
rs56163539	0.85[ASN][1000 genomes]
rs56391806	0.88[ASN][1000 genomes]
rs57131168	0.88[ASN][1000 genomes]
rs57537506	0.99[ASN][1000 genomes]
rs57893565	0.93[ASN][1000 genomes]
rs58012056	0.95[ASN][1000 genomes]
rs59045263	0.82[ASN][1000 genomes]
rs59697023	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60815228	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60825643	0.90[ASN][1000 genomes]
rs62137015	0.94[ASN][1000 genomes]
rs6545036	0.84[ASN][1000 genomes]
rs66705539	0.81[ASN][1000 genomes]
rs6705802	0.94[ASN][1000 genomes]
rs6718068	0.94[ASN][1000 genomes]
rs6722246	0.94[ASN][1000 genomes]
rs6735288	0.82[ASN][1000 genomes]
rs6743757	0.93[ASN][1000 genomes]
rs6745580	0.99[ASN][1000 genomes]
rs6756596	0.92[ASN][1000 genomes]
rs72818478	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72818488	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72818491	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72818494	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72818502	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72820403	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72820404	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72820409	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72820415	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72820416	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72820418	0.97[ASN][1000 genomes]
rs72820420	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72820422	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72820423	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72820424	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72820427	0.94[ASN][1000 genomes]
rs72820433	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72820436	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72820437	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72820439	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72820441	0.91[ASN][1000 genomes]
rs72820445	0.94[ASN][1000 genomes]
rs7559431	0.88[ASN][1000 genomes]
rs7562069	0.94[ASN][1000 genomes]
rs7562816	0.90[ASN][1000 genomes]
rs7566239	0.93[ASN][1000 genomes]
rs7568574	0.81[ASN][1000 genomes]
rs7573316	0.94[ASN][1000 genomes]
rs7576964	0.94[ASN][1000 genomes]
rs7577237	0.94[ASN][1000 genomes]
rs7579932	0.94[ASN][1000 genomes]
rs7600794	0.91[ASN][1000 genomes]
rs7606104	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv874002	chr2:48547751-48610367	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv874003	chr2:48570509-48619869	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48553400-48574400	Weak transcription	Lung	lung
2	chr2:48557000-48573200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr2:48557000-48573400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:48559800-48573400	Weak transcription	Fetal Kidney	kidney
5	chr2:48559800-48573400	Weak transcription	Right Atrium	heart
6	chr2:48560600-48573600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:48562000-48573400	Weak transcription	Psoas Muscle	Psoas
8	chr2:48562000-48573400	Weak transcription	K562	blood
9	chr2:48564800-48574400	Weak transcription	Fetal Stomach	stomach
10	chr2:48566600-48573600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:48569000-48573400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:48569000-48573400	Weak transcription	Brain Germinal Matrix	brain
13	chr2:48569000-48573400	Weak transcription	Fetal Lung	lung
14	chr2:48569000-48573400	Weak transcription	Pancreas	Pancrea
15	chr2:48569000-48574400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:48569000-48580000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:48569200-48573400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:48570200-48572600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr2:48570600-48572000	Enhancers	Primary B cells from peripheral blood	blood
20	chr2:48570600-48572000	Enhancers	Fetal Thymus	thymus
21	chr2:48570600-48572000	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr2:48570600-48573400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:48570600-48573600	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr2:48570800-48572000	Flanking Active TSS	HUVEC	blood vessel
25	chr2:48570800-48572200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:48570800-48572200	Enhancers	Fetal Intestine Large	intestine
27	chr2:48570800-48572400	Flanking Active TSS	HepG2	liver
28	chr2:48570800-48573400	Weak transcription	Placenta	Placenta
29	chr2:48570800-48575600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:48570800-48577400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:48571000-48572000	Active TSS	Primary T cells fromperipheralblood	blood
32	chr2:48571000-48572200	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr2:48571000-48572400	Enhancers	Stomach Mucosa	stomach
34	chr2:48571000-48573400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr2:48571000-48573400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:48571000-48573400	Weak transcription	Left Ventricle	heart
37	chr2:48571000-48574400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:48571000-48574400	Weak transcription	Small Intestine	intestine
39	chr2:48571000-48577000	Weak transcription	Spleen	Spleen
40	chr2:48571200-48572000	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr2:48571200-48572000	Active TSS	NHLF	lung
42	chr2:48571200-48574800	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr2:48571200-48605200	Weak transcription	Colonic Mucosa	Colon
44	chr2:48571400-48572000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:48571400-48572200	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr2:48571400-48572400	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr2:48571400-48572600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr2:48571400-48573400	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr2:48571400-48573400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr2:48571600-48572000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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