Variant report

Variant	rs59370148
Chromosome Location	chr2:54949937-54949938
allele	C/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	RFX5	chr2:54949181-54951799	IMR90	lung:	n/a	chr2:54950701-54950716
2	GTF2F1	chr2:54949675-54950790	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr2:54949527-54950069	U87	brain:	n/a	n/a
4	POLR2A	chr2:54949535-54950069	U87	brain:	n/a	n/a
5	CHD2	chr2:54949866-54951299	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr2:54949700-54950705	MCF10A-Er-Src	breast:	n/a	n/a
7	SMARCC1	chr2:54949807-54951484	Hela-S3	cervix:	n/a	chr2:54950598-54950607
8	FOS	chr2:54949697-54950085	MCF10A-Er-Src	breast:	n/a	chr2:54949893-54949903 chr2:54949893-54949903 chr2:54949893-54949903
9	MTA3	chr2:54949926-54951464	GM12878	blood:	n/a	n/a
10	E2F6	chr2:54949853-54951221	K562	blood:	n/a	chr2:54950402-54950413 chr2:54950557-54950572
11	FOXA1	chr2:54949911-54950370	HepG2	liver:	n/a	n/a
12	TBP	chr2:54949826-54951040	HepG2	liver:	n/a	n/a
13	TBP	chr2:54949783-54950906	K562	blood:	n/a	n/a
14	POLR2A	chr2:54949717-54952029	Raji	blood:	n/a	n/a
15	USF2	chr2:54949794-54950041	Hela-S3	cervix:	n/a	n/a
16	ETS1	chr2:54949876-54950932	A549	lung:	n/a	chr2:54950596-54950609 chr2:54950547-54950560 chr2:54950597-54950610
17	RFX5	chr2:54949826-54951266	Hela-S3	cervix:	n/a	chr2:54950701-54950716
18	ZNF143	chr2:54949863-54950963	K562	blood:	n/a	chr2:54950598-54950607 chr2:54950535-54950554 chr2:54950600-54950609 chr2:54950540-54950558 chr2:54950605-54950620 chr2:54950598-54950616 chr2:54950401-54950411
19	TEAD4	chr2:54949831-54950711	HepG2	liver:	n/a	n/a
20	RAD21	chr2:54949764-54951129	IMR90	lung:	n/a	n/a
21	MXI1	chr2:54949356-54954156	SK-N-SH	brain:	n/a	chr2:54949674-54949689
22	STAT3	chr2:54949789-54950081	MCF10A-Er-Src	breast:	n/a	chr2:54949948-54949955
23	CEBPB	chr2:54949759-54950891	Hela-S3	cervix:	n/a	chr2:54949914-54949931 chr2:54949905-54949918
24	MYC	chr2:54949753-54950005	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr2:54949471-54951074	U87	brain:	n/a	n/a
26	MYBL2	chr2:54949779-54951665	HepG2	liver:	n/a	n/a
27	HA-E2F1	chr2:54949666-54952092	MCF-7	breast:	n/a	chr2:54952002-54952012 chr2:54949703-54949712 chr2:54952005-54952015 chr2:54952022-54952032 chr2:54950557-54950572
28	MAX	chr2:54949727-54951255	Hela-S3	cervix:	n/a	n/a
29	FOS	chr2:54949690-54950072	MCF10A-Er-Src	breast:	n/a	chr2:54949893-54949903 chr2:54949893-54949903 chr2:54949893-54949903
30	MAFK	chr2:54949919-54950747	Hela-S3	cervix:	n/a	n/a
31	MYC	chr2:54949881-54951016	K562	blood:	n/a	n/a
32	FOS	chr2:54949715-54950061	MCF10A-Er-Src	breast:	n/a	chr2:54949893-54949903 chr2:54949893-54949903 chr2:54949893-54949903
33	RFX5	chr2:54949786-54952096	SK-N-SH	brain:	n/a	chr2:54950701-54950716
34	MAX	chr2:54949888-54951210	K562	blood:	n/a	n/a
35	SMC3	chr2:54949772-54951580	Hela-S3	cervix:	n/a	chr2:54950012-54950019
36	CEBPB	chr2:54949719-54950464	IMR90	lung:	n/a	chr2:54949914-54949931 chr2:54949905-54949918
37	MXI1	chr2:54949859-54951283	HepG2	liver:	n/a	n/a
38	POLR2A	chr2:54949801-54951043	IMR90	lung:	n/a	n/a
39	HCFC1	chr2:54949547-54951672	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr2:54949584-54951068	U87	brain:	n/a	n/a
41	POLR2A	chr2:54949839-54951000	Hela-S3	cervix:	n/a	n/a
42	SREBP1	chr2:54949596-54951061	GM12878	blood:	n/a	n/a
43	BCL3	chr2:54949809-54951114	A549	lung:	n/a	n/a
44	MBD4	chr2:54949636-54950619	HepG2	liver:	n/a	n/a
45	POLR2A	chr2:54949797-54951151	HepG2	liver:	n/a	n/a
46	MAX	chr2:54949795-54952040	A549	lung:	n/a	n/a
47	E2F4	chr2:54949651-54951116	MCF10A-Er-Src	breast:	n/a	chr2:54949703-54949712 chr2:54950781-54950792 chr2:54950557-54950572
48	POLR2A	chr2:54949557-54950675	MCF10A-Er-Src	breast:	n/a	n/a
49	TEAD4	chr2:54949937-54950714	K562	blood:	n/a	n/a
50	MXI1	chr2:54949594-54952119	IMR90	lung:	n/a	chr2:54949674-54949689

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54785416..54786973-chr2:54949128..54950959,2	K562	blood:

Variant related genes	Relation type
EML6	TF binding region
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10169328	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10170283	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175711	0.84[ASN][1000 genomes]
rs13396897	0.84[ASN][1000 genomes]
rs13399055	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13422098	0.84[ASN][1000 genomes]
rs3820856	0.84[EUR][1000 genomes]
rs60307496	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6705193	0.91[EUR][1000 genomes]
rs6740018	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72911575	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72911576	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72913513	0.83[AMR][1000 genomes]
rs72913519	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs72913521	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7560775	0.84[ASN][1000 genomes]
rs7561112	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7587575	0.93[EUR][1000 genomes];0.87[ASN][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	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1005449	chr2:54938633-55129503	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54945200-54950000	Weak transcription	Right Atrium	heart
2	chr2:54949400-54950400	Flanking Active TSS	K562	blood
3	chr2:54949600-54950000	Flanking Active TSS	H9 Cell Line	embryonic stem cell
4	chr2:54949600-54950000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:54949600-54950000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr2:54949600-54950000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:54949600-54950000	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr2:54949600-54950000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr2:54949600-54950000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:54949600-54950000	Enhancers	Fetal Muscle Leg	muscle
11	chr2:54949600-54950000	Enhancers	Stomach Mucosa	stomach
12	chr2:54949600-54950000	Flanking Active TSS	A549	lung
13	chr2:54949600-54950000	Flanking Active TSS	HepG2	liver
14	chr2:54949600-54950200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:54949600-54950200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr2:54949600-54950200	Flanking Active TSS	Brain Angular Gyrus	brain
17	chr2:54949600-54950200	Flanking Active TSS	Hela-S3	cervix
18	chr2:54949600-54950200	Flanking Active TSS	NHEK	skin
19	chr2:54949600-54950400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:54949600-54950400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:54949600-54950400	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr2:54949600-54950400	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr2:54949600-54950400	Flanking Active TSS	Dnd41	blood
24	chr2:54949600-54950400	Flanking Active TSS	Osteobl	bone
25	chr2:54949600-54950800	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr2:54949600-54950800	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr2:54949600-54951200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:54949600-54951400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
29	chr2:54949800-54950000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr2:54949800-54950000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:54949800-54950000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:54949800-54950000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:54949800-54950000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:54949800-54950000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:54949800-54950000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
36	chr2:54949800-54950000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:54949800-54950000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
38	chr2:54949800-54950000	Bivalent/Poised TSS	Primary B cells from cord blood	blood
39	chr2:54949800-54950000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
40	chr2:54949800-54950000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
41	chr2:54949800-54950000	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr2:54949800-54950000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:54949800-54950000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:54949800-54950000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr2:54949800-54950000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:54949800-54950000	Enhancers	Liver	Liver
47	chr2:54949800-54950000	Active TSS	Fetal Brain Male	brain
48	chr2:54949800-54950000	Flanking Active TSS	Fetal Intestine Small	intestine
49	chr2:54949800-54950000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr2:54949800-54950000	Flanking Bivalent TSS/Enh	Fetal Lung	lung

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