Variant report

Variant	rs2474611
Chromosome Location	chr10:52181051-52181052
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:89)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:89 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr10:52181027-52181383	K562	blood:	n/a	n/a
2	SPI1	chr10:52181011-52181548	HL-60	blood:	n/a	n/a
3	JUND	chr10:52181029-52181368	K562	blood:	n/a	n/a
4	RAD21	chr10:52181012-52181374	HepG2	liver:	n/a	n/a
5	ZNF384	chr10:52181043-52181258	K562	blood:	n/a	n/a
6	RAD21	chr10:52180995-52181398	Hela-S3	cervix:	n/a	n/a
7	MYC	chr10:52181030-52181401	K562	blood:	n/a	n/a
8	RAD21	chr10:52180910-52181543	HCT-116	colon:	n/a	n/a
9	MAX	chr10:52181049-52181247	K562	blood:	n/a	n/a
10	BATF	chr10:52181015-52181362	GM12878	blood:	n/a	n/a
11	ZNF143	chr10:52181023-52181598	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr10:52181008-52181428	IMR90	lung:	n/a	n/a
13	RAD21	chr10:52180950-52181432	GM12878	blood:	n/a	n/a
14	MYC	chr10:52181025-52181463	NB4	blood:	n/a	n/a
15	PAX5	chr10:52180957-52181364	GM12891	blood:	n/a	n/a
16	BCLAF1	chr10:52180882-52181459	GM12878	blood:	n/a	n/a
17	RAD21	chr10:52180972-52181386	H1-hESC	embryonic stem cell:	n/a	n/a
18	PAX5	chr10:52181024-52181343	GM12892	blood:	n/a	n/a
19	SMC3	chr10:52181000-52181384	K562	blood:	n/a	n/a
20	RAD21	chr10:52180914-52181488	A549	lung:	n/a	n/a
21	SMC3	chr10:52181011-52181393	Hela-S3	cervix:	n/a	n/a
22	ELF1	chr10:52180975-52181387	GM12878	blood:	n/a	chr10:52181276-52181289
23	RAD21	chr10:52180890-52181538	MCF-7	breast:	n/a	n/a
24	CTCF	chr10:52180739-52181579	A549	lung:	n/a	n/a
25	CTCF	chr10:52180867-52181717	SK-N-SH	brain:	n/a	n/a
26	SMC3	chr10:52180481-52181538	SK-N-SH	brain:	n/a	n/a
27	CTCF	chr10:52181048-52181399	H1-hESC	embryonic stem cell:	n/a	n/a
28	RAD21	chr10:52181012-52181353	SK-N-SH_RA	brain:	n/a	n/a
29	CTCF	chr10:52180992-52181382	A549	lung:	n/a	n/a
30	EBF1	chr10:52181008-52181728	GM12878	blood:	n/a	n/a
31	EP300	chr10:52180844-52181375	GM12878	blood:	n/a	n/a
32	RAD21	chr10:52180946-52181453	MCF-7	breast:	n/a	n/a
33	RAD21	chr10:52180885-52181467	A549	lung:	n/a	n/a
34	PAX5	chr10:52180914-52181397	GM12878	blood:	n/a	n/a
35	CTCF	chr10:52181007-52181304	A549	lung:	n/a	n/a
36	ZMIZ1	chr10:52180969-52181227	K562	blood:	n/a	n/a
37	STAT5A	chr10:52180920-52181364	K562	blood:	n/a	n/a
38	CTCF	chr10:52180968-52181418	HepG2	liver:	n/a	n/a
39	RAD21	chr10:52180931-52181413	H1-hESC	embryonic stem cell:	n/a	n/a
40	TEAD4	chr10:52181006-52181418	ECC-1	luminal epithelium:	n/a	n/a
41	CTCF	chr10:52180768-52181434	K562	blood:	n/a	n/a
42	TBP	chr10:52181047-52181385	K562	blood:	n/a	n/a
43	MAZ	chr10:52181044-52181387	Hela-S3	cervix:	n/a	n/a
44	RAD21	chr10:52180870-52181561	SK-N-SH	brain:	n/a	n/a
45	PAX5	chr10:52180913-52181368	GM12878	blood:	n/a	n/a
46	BHLHE40	chr10:52181029-52181341	K562	blood:	n/a	n/a
47	TBL1XR1	chr10:52181026-52181604	GM12878	blood:	n/a	n/a
48	CTCF	chr10:52181044-52181326	HepG2	liver:	n/a	n/a
49	CTCF	chr10:52180890-52181441	HCT-116	colon:	n/a	n/a
50	CTCF	chr10:52181008-52181383	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52127277..52127980-chr10:52180802..52181438,3	MCF-7	breast:
2	chr10:52181046..52183288-chr10:52255236..52257097,2	MCF-7	breast:
3	chr10:52127262..52128152-chr10:52180974..52181673,2	K562	blood:
4	chr10:52175389..52176966-chr10:52179598..52182050,2	K562	blood:
5	chr10:52180307..52183169-chr10:52383906..52386239,2	K562	blood:
6	chr10:52179920..52182656-chr10:52203017..52204731,2	K562	blood:
7	chr10:52179209..52181843-chr10:52226952..52229570,2	MCF-7	breast:
8	chr10:52176749..52178866-chr10:52179847..52182390,3	MCF-7	breast:
9	chr10:52180808..52181738-chr10:52309939..52310789,2	K562	blood:
10	chr10:52050989..52051888-chr10:52180720..52181237,2	K562	blood:

No data

Variant related genes	Relation type
SGMS1	TF binding region
ENSG00000198964	Chromatin interaction
ENSG00000226200	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1203374	1.00[ASN][1000 genomes]
rs1203378	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1203379	1.00[ASN][1000 genomes]
rs1203383	1.00[ASN][1000 genomes]
rs1203384	1.00[ASN][1000 genomes]
rs1203391	1.00[ASN][1000 genomes]
rs1203402	1.00[ASN][1000 genomes]
rs1203412	1.00[ASN][1000 genomes]
rs1203416	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203417	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203422	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203427	1.00[ASN][1000 genomes]
rs1211373	1.00[ASN][1000 genomes]
rs2024871	1.00[ASN][1000 genomes]
rs2208035	1.00[ASN][1000 genomes]
rs2574945	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2574976	1.00[ASN][1000 genomes]
rs2688874	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688876	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688883	1.00[ASN][1000 genomes]
rs2688884	1.00[ASN][1000 genomes]
rs2842099	1.00[ASN][1000 genomes]
rs2842110	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983348	1.00[ASN][1000 genomes]
rs2983372	1.00[ASN][1000 genomes]
rs3011712	1.00[ASN][1000 genomes]
rs3011715	1.00[ASN][1000 genomes]
rs3011768	1.00[ASN][1000 genomes]
rs3011795	1.00[ASN][1000 genomes]
rs72801753	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7923756	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910819	1.00[ASN][1000 genomes]
rs9416590	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv521273	chr10:52051645-52197847	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 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	chr10:52178400-52220000	Weak transcription	Pancreas	Pancrea
2	chr10:52178600-52181200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr10:52178600-52181400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr10:52178600-52181400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr10:52178600-52181400	Weak transcription	Gastric	stomach
6	chr10:52178600-52181400	Weak transcription	Lung	lung
7	chr10:52178600-52181600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr10:52178600-52181600	Weak transcription	Fetal Stomach	stomach
9	chr10:52178600-52181800	Weak transcription	Fetal Brain Female	brain
10	chr10:52178600-52182000	Enhancers	Brain Hippocampus Middle	brain
11	chr10:52178600-52182400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr10:52178600-52182600	Enhancers	Fetal Lung	lung
13	chr10:52178600-52183400	Enhancers	Brain Cingulate Gyrus	brain
14	chr10:52178600-52188800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr10:52178600-52217200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr10:52178600-52219400	Weak transcription	Left Ventricle	heart
17	chr10:52178800-52181200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr10:52178800-52181600	Enhancers	Brain Substantia Nigra	brain
19	chr10:52178800-52181600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr10:52178800-52182000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr10:52178800-52182400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr10:52178800-52183800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr10:52178800-52187400	Weak transcription	Primary T cells from cord blood	blood
24	chr10:52178800-52191200	Weak transcription	HSMMtube	muscle
25	chr10:52178800-52198000	Weak transcription	Fetal Thymus	thymus
26	chr10:52178800-52202800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr10:52179000-52181600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr10:52179000-52191000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr10:52179000-52191200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr10:52179000-52191400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr10:52179000-52191600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr10:52179000-52205800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr10:52179000-52207600	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr10:52179000-52209000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr10:52179200-52181400	Weak transcription	Adipose Nuclei	Adipose
36	chr10:52179200-52181600	Enhancers	K562	blood
37	chr10:52179200-52181800	Weak transcription	Osteobl	bone
38	chr10:52179200-52196600	Weak transcription	Colon Smooth Muscle	Colon
39	chr10:52179600-52181200	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr10:52179600-52181800	Enhancers	Right Atrium	heart
41	chr10:52179600-52183400	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr10:52179800-52181400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr10:52179800-52181400	Weak transcription	Liver	Liver
44	chr10:52180000-52181400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr10:52180000-52182200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr10:52180000-52185000	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr10:52180000-52189800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr10:52180000-52190800	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr10:52180200-52181800	Weak transcription	NHLF	lung
50	chr10:52180200-52201200	Weak transcription	Fetal Heart	heart

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