Variant report

Variant	rs1203419
Chromosome Location	chr10:52182312-52182313
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	ATF2	chr10:52182049-52182522	GM12878	blood:	n/a	n/a
2	IKZF1	chr10:52182110-52182495	GM12878	blood:	n/a	n/a
3	EP300	chr10:52182127-52182313	GM12878	blood:	n/a	chr10:52182243-52182252
4	CUX1	chr10:52182214-52182445	GM12878	blood:	n/a	n/a
5	SPI1	chr10:52182065-52182408	GM12878	blood:	n/a	chr10:52182241-52182254
6	BHLHE40	chr10:52182183-52182343	GM12878	blood:	n/a	n/a
7	SPI1	chr10:52182066-52182454	GM12891	blood:	n/a	chr10:52182241-52182254
8	SPI1	chr10:52182143-52182389	GM12878	blood:	n/a	chr10:52182241-52182254

No.	Distal block	Cell Line	Cell type
1	chr10:52181046..52183288-chr10:52255236..52257097,2	MCF-7	breast:
2	chr10:52181748..52183434-chr10:52188510..52191185,2	MCF-7	breast:
3	chr10:52182056..52184525-chr10:52364290..52366109,2	MCF-7	breast:
4	chr10:52180307..52183169-chr10:52383906..52386239,2	K562	blood:
5	chr10:52179920..52182656-chr10:52203017..52204731,2	K562	blood:
6	chr10:52176794..52179947-chr10:52182288..52185320,3	K562	blood:
7	chr10:52176749..52178866-chr10:52179847..52182390,3	MCF-7	breast:

Variant related genes	Relation type
SGMS1	TF binding region
ENSG00000226200	Chromatin interaction
ENSG00000230036	Chromatin interaction
ENSG00000198964	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]
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]
rs2474611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];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:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52178400-52220000	Weak transcription	Pancreas	Pancrea
2	chr10:52178600-52182400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr10:52178600-52182600	Enhancers	Fetal Lung	lung
4	chr10:52178600-52183400	Enhancers	Brain Cingulate Gyrus	brain
5	chr10:52178600-52188800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr10:52178600-52217200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr10:52178600-52219400	Weak transcription	Left Ventricle	heart
8	chr10:52178800-52182400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr10:52178800-52183800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr10:52178800-52187400	Weak transcription	Primary T cells from cord blood	blood
11	chr10:52178800-52191200	Weak transcription	HSMMtube	muscle
12	chr10:52178800-52198000	Weak transcription	Fetal Thymus	thymus
13	chr10:52178800-52202800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr10:52179000-52191000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr10:52179000-52191200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr10:52179000-52191400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr10:52179000-52191600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr10:52179000-52205800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr10:52179000-52207600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr10:52179000-52209000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr10:52179200-52196600	Weak transcription	Colon Smooth Muscle	Colon
22	chr10:52179600-52183400	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr10:52180000-52185000	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr10:52180000-52189800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr10:52180000-52190800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr10:52180200-52201200	Weak transcription	Fetal Heart	heart
27	chr10:52180600-52182400	Flanking Active TSS	GM12878-XiMat	blood
28	chr10:52180600-52194000	Weak transcription	Fetal Intestine Large	intestine
29	chr10:52181000-52182600	Enhancers	Stomach Mucosa	stomach
30	chr10:52181000-52182800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr10:52181000-52183000	Enhancers	Brain Angular Gyrus	brain
32	chr10:52181200-52182600	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr10:52181400-52182400	Enhancers	Adipose Nuclei	Adipose
34	chr10:52181400-52184000	Enhancers	Liver	Liver
35	chr10:52181400-52191000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr10:52181600-52182600	Enhancers	Brain Germinal Matrix	brain
37	chr10:52181600-52184000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr10:52181600-52184800	Weak transcription	Primary B cells from cord blood	blood
39	chr10:52181600-52187200	Weak transcription	K562	blood
40	chr10:52181600-52187800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr10:52181600-52189800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr10:52181600-52190800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr10:52181600-52219400	Weak transcription	Placenta	Placenta
44	chr10:52181800-52182400	Enhancers	NHLF	lung
45	chr10:52181800-52182800	Weak transcription	Spleen	Spleen
46	chr10:52181800-52183000	Enhancers	Fetal Brain Female	brain
47	chr10:52181800-52183800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr10:52181800-52206200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr10:52182000-52182400	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr10:52182000-52182400	Flanking Active TSS	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links