Variant report

Variant	rs12360409
Chromosome Location	chr10:5975798-5975799
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	GATA1	chr10:5975745-5976410	K562	blood:	n/a	chr10:5976092-5976113 chr10:5976136-5976145
2	ZNF384	chr10:5975562-5976445	K562	blood:	n/a	n/a
3	CBX3	chr10:5975756-5976303	K562	blood:	n/a	n/a
4	MAX	chr10:5975759-5976185	K562	blood:	n/a	n/a
5	GATA1	chr10:5975218-5976493	PBDE	blood:	n/a	chr10:5976092-5976113 chr10:5976136-5976145

No.	Distal block	Cell Line	Cell type
1	chr10:5971270..5973563-chr10:5974618..5977378,2	K562	blood:
2	chr10:5973930..5977726-chr10:5979603..5983323,6	K562	blood:
3	chr10:5964443..5967389-chr10:5974579..5977579,3	K562	blood:
4	chr10:5965483..5967118-chr10:5975794..5977895,2	MCF-7	breast:
5	chr10:5930031..5932974-chr10:5974557..5976275,2	MCF-7	breast:

Variant related genes	Relation type
FBXO18	TF binding region
ENSG00000134452	Chromatin interaction
ENSG00000134461	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10508298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10508299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255698	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255774	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11255974	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11256009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359234	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12767690	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12777477	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12781700	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12785055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17319759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976655	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985072	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2387092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36049919	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3891620	0.94[YRI][hapmap]
rs56369297	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61832959	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6602330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7067928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7893735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7919913	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];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	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats 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	42 gene(s)	inside rSNPs	diseases
2	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1041261	chr10:5962635-6052196	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1050983	chr10:5963921-6052196	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5933200-5977000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:5944000-5981600	Strong transcription	Fetal Intestine Small	intestine
3	chr10:5944600-5981200	Strong transcription	Fetal Thymus	thymus
4	chr10:5945800-5980800	Strong transcription	Thymus	Thymus
5	chr10:5947000-5980800	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr10:5947000-5981600	Strong transcription	Placenta	Placenta
7	chr10:5947200-5981000	Strong transcription	Fetal Intestine Large	intestine
8	chr10:5947400-5981200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr10:5947600-5981000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:5947600-5981000	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr10:5947600-5981000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr10:5947600-5981000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr10:5947600-5981200	Strong transcription	Primary B cells from peripheral blood	blood
14	chr10:5948000-5975800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr10:5948400-5981000	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr10:5948400-5981000	Strong transcription	Stomach Smooth Muscle	stomach
17	chr10:5948600-5981000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr10:5948800-5981000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr10:5948800-5981000	Strong transcription	Duodenum Mucosa	Duodenum
20	chr10:5948800-5981600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr10:5950000-5976400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr10:5950000-5980400	Strong transcription	Dnd41	blood
23	chr10:5950200-5975800	Strong transcription	Brain Germinal Matrix	brain
24	chr10:5950200-5981000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr10:5950600-5981000	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr10:5950600-5981000	Strong transcription	Lung	lung
27	chr10:5950600-5981000	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr10:5950600-5981200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr10:5950800-5980600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr10:5950800-5980800	Strong transcription	GM12878-XiMat	blood
31	chr10:5952000-5985000	Weak transcription	Stomach Mucosa	stomach
32	chr10:5955000-5981400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr10:5960600-5977800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr10:5960600-5977800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr10:5960600-5981200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr10:5961000-5981200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr10:5965800-5981000	Strong transcription	A549	lung
38	chr10:5966200-5983600	Weak transcription	Right Atrium	heart
39	chr10:5969400-5982800	Strong transcription	Fetal Stomach	stomach
40	chr10:5969600-5977800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr10:5969600-5987800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr10:5969600-6012000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr10:5969800-5980800	Strong transcription	HSMMtube	muscle
44	chr10:5969800-5981000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr10:5969800-5981200	Strong transcription	Fetal Muscle Leg	muscle
46	chr10:5970000-5981600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr10:5970200-5976200	Strong transcription	NHLF	lung
48	chr10:5970400-5981000	Strong transcription	Osteobl	bone
49	chr10:5971200-5977200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr10:5971200-5981000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links