Variant report

Variant	rs1567706
Chromosome Location	chr10:5853767-5853768
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr10:5853079-5854877	K562	blood:	n/a	chr10:5853931-5853947
2	MXI1	chr10:5852991-5857043	SK-N-SH	brain:	n/a	chr10:5855794-5855803 chr10:5855794-5855803 chr10:5855796-5855805
3	ZNF384	chr10:5853408-5853834	K562	blood:	n/a	n/a
4	POLR2A	chr10:5852865-5857536	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr10:5853265-5856938	IMR90	lung:	n/a	n/a
6	POLR2A	chr10:5853116-5853822	HepG2	liver:	n/a	n/a
7	PBX3	chr10:5853419-5853869	SK-N-SH	brain:	n/a	n/a
8	IRF1	chr10:5853729-5854672	K562	blood:	n/a	chr10:5853931-5853947
9	CHD1	chr10:5853304-5855391	H1-hESC	embryonic stem cell:	n/a	chr10:5854926-5854936 chr10:5854992-5855002 chr10:5855258-5855265
10	POLR2A	chr10:5851288-5853864	HepG2	liver:	n/a	n/a
11	HEY1	chr10:5853392-5853770	HepG2	liver:	n/a	n/a
12	POLR2A	chr10:5852378-5856984	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:5853439..5857708-chr10:5926443..5936823,24	K562	blood:
2	chr10:5769286..5771166-chr10:5852816..5855046,2	K562	blood:
3	chr10:5853185..5855023-chr10:5896110..5898472,2	K562	blood:
4	chr10:5852473..5857853-chr10:5880942..5888645,8	MCF-7	breast:
5	chr10:5711853..5714027-chr10:5850909..5854727,3	K562	blood:
6	chr10:5487246..5491032-chr10:5851403..5854778,3	K562	blood:
7	chr10:5853517..5856397-chr10:6017987..6020051,2	MCF-7	breast:
8	chr10:5853575..5857221-chr10:5900529..5905112,5	MCF-7	breast:
9	chr10:5487976..5490601-chr10:5853120..5856110,3	MCF-7	breast:
10	chr10:5831817..5834005-chr10:5852525..5854271,2	K562	blood:
11	chr10:5834748..5836867-chr10:5852266..5855152,2	K562	blood:
12	chr10:5810933..5813093-chr10:5852041..5854972,2	K562	blood:
13	chr10:5851570..5858995-chr10:5881654..5887342,9	K562	blood:
14	chr10:5805727..5811403-chr10:5852267..5856532,7	MCF-7	breast:
15	chr10:5707157..5710880-chr10:5853405..5856185,3	K562	blood:
16	chr10:5813790..5816403-chr10:5853643..5855335,2	MCF-7	breast:
17	chr10:5719546..5721804-chr10:5852242..5853949,2	K562	blood:
18	chr10:5815026..5819070-chr10:5852954..5857275,5	MCF-7	breast:
19	chr10:5850869..5856128-chr10:5879241..5885807,8	K562	blood:
20	chr10:5725427..5729550-chr10:5853446..5856157,4	MCF-7	breast:
21	chr10:5853267..5855548-chr10:5881785..5884894,3	MCF-7	breast:
22	chr10:5852595..5861125-chr10:5921136..5936216,31	MCF-7	breast:
23	chr10:5852308..5856409-chr10:5935538..5939554,4	K562	blood:
24	chr10:5853532..5857435-chr10:5928623..5934190,13	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272764	TF binding region
ENSG00000196372	Chromatin interaction
ENSG00000134461	Chromatin interaction
ENSG00000134470	Chromatin interaction
ENSG00000108021	Chromatin interaction
ENSG00000134452	Chromatin interaction
ENSG00000057608	Chromatin interaction
ENSG00000240180	Chromatin interaction
ENSG00000173848	Chromatin interaction
ENSG00000270427	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10737012	0.84[EUR][1000 genomes]
rs10752110	0.87[EUR][1000 genomes]
rs10752111	0.83[EUR][1000 genomes]
rs10795347	0.83[CEU][hapmap]
rs10795485	0.84[EUR][1000 genomes]
rs10795488	0.83[EUR][1000 genomes]
rs10795510	0.84[EUR][1000 genomes]
rs10795541	0.96[CEU][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs10905065	0.88[CEU][hapmap];0.93[TSI][hapmap]
rs10905137	0.81[EUR][1000 genomes]
rs11254266	0.80[ASW][hapmap];0.82[CHB][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap]
rs11255228	0.86[EUR][1000 genomes]
rs11598374	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12571639	0.85[EUR][1000 genomes]
rs1567707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1858447	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967487	0.81[EUR][1000 genomes]
rs2175630	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2244755	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs2380199	0.84[CEU][hapmap]
rs2380202	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2380203	0.87[CEU][hapmap]
rs2497	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2797488	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2890365	0.96[CEU][hapmap];0.95[TSI][hapmap]
rs2892078	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3736462	0.81[EUR][1000 genomes]
rs4237365	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4748913	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4748916	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60840965	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6602240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6602259	0.83[EUR][1000 genomes]
rs6602278	0.88[TSI][hapmap]
rs7071811	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7078711	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7089100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7096742	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7100576	0.80[EUR][1000 genomes]
rs7896749	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7906719	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7909733	0.82[EUR][1000 genomes]
rs7909988	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7913067	0.88[CEU][hapmap];0.93[TSI][hapmap]
rs7916827	0.83[EUR][1000 genomes]
rs9423726	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9423930	0.82[EUR][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	nsv515935	chr10:5820394-5869839	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv549896	chr10:5820394-5880066	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1567706	GDI2	cis	cerebellum	SCAN
rs1567706	GDI2	cis	parietal	SCAN
rs1567706	GDI2	cis	uninvolved skin	skin_eQTL
rs1567706	GDI2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5818000-5854200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:5837800-5854200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:5843600-5854400	Weak transcription	Gastric	stomach
4	chr10:5847600-5854600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr10:5848800-5854200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr10:5850200-5854600	Weak transcription	Spleen	Spleen
7	chr10:5851200-5853800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr10:5851200-5854000	Enhancers	Placenta Amnion	Placenta Amnion
9	chr10:5851200-5854800	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr10:5851200-5854800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr10:5851400-5854000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr10:5851400-5854200	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr10:5851400-5854400	Flanking Active TSS	HUVEC	blood vessel
14	chr10:5851600-5854200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr10:5851600-5856200	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr10:5851800-5854600	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr10:5851800-5856000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr10:5852000-5854600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr10:5852000-5855800	Active TSS	HMEC	breast
20	chr10:5852000-5856800	Active TSS	NHLF	lung
21	chr10:5852400-5853800	Flanking Active TSS	Fetal Brain Female	brain
22	chr10:5852400-5854200	Weak transcription	Stomach Mucosa	stomach
23	chr10:5852400-5854400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr10:5852400-5854600	Flanking Active TSS	Liver	Liver
25	chr10:5852400-5854800	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr10:5852400-5854800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr10:5852400-5856600	Active TSS	H1 Cell Line	embryonic stem cell
28	chr10:5852600-5854000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr10:5852600-5854400	Weak transcription	Small Intestine	intestine
30	chr10:5852600-5854600	Active TSS	Right Atrium	heart
31	chr10:5852600-5856200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr10:5852600-5856400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr10:5852600-5856800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr10:5852800-5854400	Active TSS	HepG2	liver
35	chr10:5852800-5854800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr10:5852800-5854800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr10:5852800-5856400	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr10:5852800-5856800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr10:5853000-5853800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr10:5853000-5853800	Flanking Active TSS	Fetal Heart	heart
41	chr10:5853000-5854200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr10:5853000-5854600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr10:5853000-5856000	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr10:5853000-5856000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr10:5853000-5856000	Active TSS	Fetal Intestine Large	intestine
46	chr10:5853000-5856000	Active TSS	GM12878-XiMat	blood
47	chr10:5853000-5856000	Active TSS	NH-A	brain
48	chr10:5853000-5856200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr10:5853000-5856200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr10:5853000-5856200	Active TSS	Primary T helper cells PMA-I stimulated	--

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