Variant report

Variant	rs7900361
Chromosome Location	chr10:5856984-5856985
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:5854614-5857010	GM19193	blood:	n/a	n/a
2	MXI1	chr10:5852991-5857043	SK-N-SH	brain:	n/a	chr10:5855794-5855803 chr10:5855794-5855803 chr10:5855796-5855805
3	POLR2A	chr10:5856731-5857043	K562	blood:	n/a	n/a
4	POLR2A	chr10:5856529-5857045	GM12891	blood:	n/a	n/a
5	POLR2A	chr10:5852865-5857536	MCF10A-Er-Src	breast:	n/a	n/a
6	ESRRA	chr10:5853937-5857177	GM12878	blood:	n/a	chr10:5855737-5855749 chr10:5854470-5854482 chr10:5854465-5854481
7	POLR2A	chr10:5854618-5857409	GM18951	blood:	n/a	n/a
8	POLR2A	chr10:5853823-5857228	GM12878	blood:	n/a	n/a
9	POLR2A	chr10:5854191-5857525	GM12892	blood:	n/a	n/a
10	POLR2A	chr10:5854313-5857041	GM12892	blood:	n/a	n/a
11	POLR2A	chr10:5856519-5857149	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr10:5854646-5856995	U87	brain:	n/a	n/a
13	POLR2A	chr10:5854147-5859027	GM12891	blood:	n/a	n/a
14	POLR2A	chr10:5856766-5857361	GM12891	blood:	n/a	n/a
15	POLR2A	chr10:5855185-5857664	K562	blood:	n/a	n/a
16	POLR2A	chr10:5854582-5857443	K562	blood:	n/a	n/a
17	POLR2A	chr10:5854697-5857370	K562	blood:	n/a	n/a
18	POLR2A	chr10:5856741-5857466	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr10:5856695-5857047	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr10:5854387-5857333	K562	blood:	n/a	n/a
21	POLR2A	chr10:5854182-5857522	GM12878	blood:	n/a	n/a
22	POLR2A	chr10:5854462-5858661	Raji	blood:	n/a	n/a
23	POLR2A	chr10:5856951-5857469	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr10:5854799-5857185	NB4	blood:	n/a	n/a
25	POLR2A	chr10:5856624-5857691	HepG2	liver:	n/a	n/a
26	POLR2A	chr10:5854288-5856987	K562	blood:	n/a	n/a
27	POLR2A	chr10:5854306-5857324	GM19099	blood:	n/a	n/a
28	POLR2A	chr10:5854416-5857032	K562	blood:	n/a	n/a
29	POLR2A	chr10:5856754-5857691	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr10:5854182-5857602	GM12878	blood:	n/a	n/a
31	POLR2A	chr10:5856655-5857570	GM12878	blood:	n/a	n/a
32	POLR2A	chr10:5852378-5856984	MCF10A-Er-Src	breast:	n/a	n/a
33	MXI1	chr10:5854360-5857069	IMR90	lung:	n/a	chr10:5855794-5855803 chr10:5855794-5855803 chr10:5855796-5855805
34	POLR2A	chr10:5854462-5857077	MCF-7	breast:	n/a	n/a
35	POLR2A	chr10:5854209-5857035	K562	blood:	n/a	n/a
36	POLR2A	chr10:5854215-5857590	GM12892	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:5725503..5729426-chr10:5853777..5860412,5	MCF-7	breast:
2	chr10:5853439..5857708-chr10:5926443..5936823,24	K562	blood:
3	chr10:5852473..5857853-chr10:5880942..5888645,8	MCF-7	breast:
4	chr10:5853575..5857221-chr10:5900529..5905112,5	MCF-7	breast:
5	chr10:5732056..5734929-chr10:5855542..5857938,2	K562	blood:
6	chr10:5664947..5667027-chr10:5854331..5857046,2	MCF-7	breast:
7	chr10:5851570..5858995-chr10:5881654..5887342,9	K562	blood:
8	chr10:5855633..5857899-chr8:144821553..144823070,2	MCF-7	breast:
9	chr10:5815026..5819070-chr10:5852954..5857275,5	MCF-7	breast:
10	chr10:5725239..5729489-chr10:5854026..5858186,8	K562	blood:
11	chr10:5852595..5861125-chr10:5921136..5936216,31	MCF-7	breast:
12	chr10:5809711..5811648-chr10:5855446..5857250,2	K562	blood:
13	chr10:5810148..5812616-chr10:5855203..5857512,4	K562	blood:
14	chr10:5853532..5857435-chr10:5928623..5934190,13	MCF-7	breast:

No data

Variant related genes	Relation type
GDI2	TF binding region
ENSG00000108021	Chromatin interaction
ENSG00000270427	Chromatin interaction
ENSG00000203499	Chromatin interaction
ENSG00000228685	Chromatin interaction
ENSG00000134461	Chromatin interaction
ENSG00000057608	Chromatin interaction
ENSG00000134452	Chromatin interaction
ENSG00000240180	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10737018	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs10905029	0.89[EUR][1000 genomes]
rs10905066	0.95[EUR][1000 genomes]
rs2254067	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2380209	0.81[CEU][hapmap];0.92[CHB][hapmap];0.85[EUR][1000 genomes]
rs2386664	0.82[ASN][1000 genomes]
rs2669135	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[GIH][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2669137	0.90[EUR][1000 genomes]
rs2797486	1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2797487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2797491	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs2797493	0.91[EUR][1000 genomes]
rs2797494	0.91[EUR][1000 genomes]
rs2797501	0.92[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.83[TSI][hapmap]
rs4423100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61016063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7907687	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.95[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

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5853000-5857000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr10:5853200-5857000	Active TSS	H9 Cell Line	embryonic stem cell
3	chr10:5855800-5857000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr10:5856000-5857000	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr10:5856000-5857000	Flanking Active TSS	Primary B cells from peripheral blood	blood
6	chr10:5856000-5857000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr10:5856000-5857000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr10:5856000-5857200	Flanking Active TSS	Dnd41	blood
9	chr10:5856000-5857400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr10:5856000-5857400	Flanking Active TSS	GM12878-XiMat	blood
11	chr10:5856200-5857000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr10:5856200-5857000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr10:5856200-5857000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr10:5856200-5857000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr10:5856200-5857000	Flanking Active TSS	Fetal Brain Female	brain
16	chr10:5856200-5857000	Enhancers	Small Intestine	intestine
17	chr10:5856200-5857200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr10:5856200-5857400	Enhancers	Spleen	Spleen
19	chr10:5856200-5862600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr10:5856400-5857000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr10:5856400-5857000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr10:5856400-5857000	Enhancers	Brain Substantia Nigra	brain
23	chr10:5856400-5857000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr10:5856400-5857000	Enhancers	Placenta	Placenta
25	chr10:5856400-5857200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr10:5856400-5857200	Enhancers	Colon Smooth Muscle	Colon
27	chr10:5856400-5857400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr10:5856400-5857400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr10:5856400-5857400	Enhancers	Fetal Intestine Large	intestine
30	chr10:5856400-5857400	Enhancers	Fetal Intestine Small	intestine
31	chr10:5856400-5857400	Enhancers	Pancreas	Pancrea
32	chr10:5856400-5858400	Weak transcription	HSMM	muscle
33	chr10:5856400-5859000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr10:5856400-5859800	Weak transcription	Esophagus	oesophagus
35	chr10:5856600-5857000	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr10:5856600-5857000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr10:5856600-5857000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr10:5856600-5857000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr10:5856600-5857000	Enhancers	Brain Angular Gyrus	brain
40	chr10:5856600-5857000	Enhancers	Brain Hippocampus Middle	brain
41	chr10:5856600-5857000	Enhancers	Colonic Mucosa	Colon
42	chr10:5856600-5857000	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr10:5856600-5857000	Enhancers	Fetal Brain Male	brain
44	chr10:5856600-5857000	Enhancers	Fetal Stomach	stomach
45	chr10:5856600-5857000	Enhancers	Psoas Muscle	Psoas
46	chr10:5856600-5857000	Enhancers	HMEC	breast
47	chr10:5856600-5857000	Enhancers	HSMMtube	muscle
48	chr10:5856600-5857000	Enhancers	HUVEC	blood vessel
49	chr10:5856600-5857000	Enhancers	NH-A	brain
50	chr10:5856600-5857000	Enhancers	Osteobl	bone

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