Variant report

Variant	rs591510
Chromosome Location	chr10:5941953-5941954
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	POLR2A	chr10:5941929-5942242	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:5940356..5945616-chr10:5946052..5950228,5	K562	blood:
2	chr10:5934666..5939071-chr10:5940230..5944610,6	MCF-7	breast:

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

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs2274029	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs2320	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs2669122	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2669126	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs582359	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs591878	0.84[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.99[ASN][1000 genomes]
rs593610	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs595923	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598331	0.90[ASN][1000 genomes]
rs603780	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs607728	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs610093	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs621628	0.98[ASN][1000 genomes]
rs622758	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs626344	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs633797	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs633928	1.00[ASN][1000 genomes]
rs633930	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs635532	0.97[ASN][1000 genomes]
rs636578	0.88[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.96[ASN][1000 genomes]
rs647945	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs649537	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs664603	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs668498	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs670856	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs672126	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs680020	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs685852	0.99[ASN][1000 genomes]
rs686854	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs688388	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs792348	0.84[ASN][1000 genomes]
rs907687	0.84[CEU][hapmap];0.82[LWK][hapmap];0.91[MKK][hapmap]
rs980230	0.84[CEU][hapmap];0.82[LWK][hapmap];0.91[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv825229	chr10:5886905-5967697	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5933200-5948200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:5933200-5949800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr10:5933200-5977000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr10:5933400-5948200	Weak transcription	Ovary	ovary
5	chr10:5933400-5948400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr10:5933400-5949800	Weak transcription	Fetal Brain Male	brain
7	chr10:5933600-5948200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr10:5933600-5951600	Weak transcription	Stomach Mucosa	stomach
9	chr10:5934800-5948000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr10:5935200-5947400	Weak transcription	Small Intestine	intestine
11	chr10:5935600-5943000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr10:5935600-5962000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr10:5936600-5952600	Weak transcription	Hela-S3	cervix
14	chr10:5936800-5953200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr10:5937200-5947600	Weak transcription	Psoas Muscle	Psoas
16	chr10:5937200-5948000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr10:5937200-5948000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr10:5937200-5948400	Weak transcription	Fetal Kidney	kidney
19	chr10:5937400-5948200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr10:5937800-5947600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr10:5937800-5947600	Weak transcription	HSMM	muscle
22	chr10:5937800-5948000	Weak transcription	Brain Angular Gyrus	brain
23	chr10:5937800-5948200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr10:5938000-5947600	Weak transcription	HSMMtube	muscle
25	chr10:5938000-5947800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr10:5938000-5948000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr10:5938000-5948200	Weak transcription	HMEC	breast
28	chr10:5938000-5950800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr10:5938200-5944000	Weak transcription	Brain Hippocampus Middle	brain
30	chr10:5938200-5947200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr10:5938200-5947600	Weak transcription	Brain Anterior Caudate	brain
32	chr10:5938200-5947800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr10:5938200-5948000	Weak transcription	Aorta	Aorta
34	chr10:5938200-5950800	Weak transcription	NH-A	brain
35	chr10:5938400-5944000	Weak transcription	Pancreas	Pancrea
36	chr10:5938400-5945800	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr10:5938400-5947000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr10:5938400-5947600	Weak transcription	HepG2	liver
39	chr10:5938400-5947800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr10:5938400-5948000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr10:5938600-5947200	Weak transcription	Fetal Intestine Large	intestine
42	chr10:5938600-5947600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr10:5938600-5947800	Weak transcription	HUVEC	blood vessel
44	chr10:5938600-5948000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr10:5938600-5948200	Weak transcription	Brain Substantia Nigra	brain
46	chr10:5938800-5945800	Weak transcription	NHDF-Ad	bronchial
47	chr10:5938800-5947800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr10:5938800-5948000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr10:5939000-5947600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr10:5939000-5947600	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links