Variant report

Variant	rs2480782
Chromosome Location	chr1:10593296-10593297
allele	A/C
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	chr1:10592785-10593393	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:10591577..10594181-chr1:10600029..10602001,2	K562	blood:
2	chr1:10585162..10588309-chr1:10589608..10593566,5	K562	blood:
3	chr1:10577532..10580475-chr1:10590665..10593408,2	K562	blood:

Variant related genes	Relation type
PEX14	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11121587	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1188526	0.82[CHB][hapmap]
rs12028449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12375	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1307489	0.91[TSI][hapmap]
rs1307490	0.91[TSI][hapmap]
rs1307494	0.91[TSI][hapmap]
rs1307497	0.84[TSI][hapmap]
rs1411402	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs17035305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2026792	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2056417	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs2150038	0.82[ASN][1000 genomes]
rs2480777	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2480784	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2483677	1.00[ASW][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap]
rs2483686	0.91[TSI][hapmap]
rs2506889	0.82[ASN][1000 genomes]
rs2506892	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2847337	0.91[TSI][hapmap]
rs4845937	0.83[EUR][1000 genomes]
rs585870	0.82[CHB][hapmap]
rs589400	0.90[CHB][hapmap]
rs596537	0.82[CHB][hapmap]
rs607941	0.82[CHB][hapmap]
rs620405	0.82[CHB][hapmap]
rs622623	0.82[CHB][hapmap]
rs647281	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs648324	0.82[CHB][hapmap]
rs648399	0.82[CHB][hapmap]
rs660725	0.82[CHB][hapmap]
rs662064	0.82[CHB][hapmap]
rs666103	1.00[TSI][hapmap]
rs6687430	0.86[JPT][hapmap]
rs668805	0.82[CHB][hapmap]
rs669701	0.82[CHB][hapmap]
rs67488812	0.82[ASN][1000 genomes]
rs9430149	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv2521	chr1:10553530-10598171	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv545395	chr1:10584672-10613660	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10570800-10595600	Weak transcription	Primary B cells from cord blood	blood
2	chr1:10572200-10598600	Weak transcription	Brain Anterior Caudate	brain
3	chr1:10573400-10596000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr1:10576400-10596000	Weak transcription	Dnd41	blood
5	chr1:10577000-10603600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:10577400-10596400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:10579400-10610200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:10579600-10596200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:10580800-10596000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:10580800-10596200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:10582600-10595800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr1:10582600-10596200	Weak transcription	Thymus	Thymus
13	chr1:10583000-10595800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:10584400-10596000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:10584600-10594200	Weak transcription	K562	blood
16	chr1:10584800-10603800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:10585200-10603600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:10585200-10603800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:10586200-10595600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr1:10588400-10596200	Weak transcription	Lung	lung
21	chr1:10588400-10598200	Weak transcription	Pancreas	Pancrea
22	chr1:10588600-10596400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:10588800-10596400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:10588800-10599200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:10589000-10596400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:10589000-10600000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:10589200-10598600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:10589400-10595600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:10589400-10596200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:10589400-10596200	Weak transcription	Esophagus	oesophagus
31	chr1:10589400-10596400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:10589400-10664800	Weak transcription	Aorta	Aorta
33	chr1:10589600-10596000	Weak transcription	Primary T cells from cord blood	blood
34	chr1:10590200-10595600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:10590200-10595800	Weak transcription	HepG2	liver
36	chr1:10590200-10596200	Weak transcription	Fetal Intestine Large	intestine
37	chr1:10590200-10596400	Weak transcription	Gastric	stomach
38	chr1:10590200-10597200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:10590200-10602800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:10590200-10605200	Weak transcription	NHDF-Ad	bronchial
41	chr1:10590600-10596000	Weak transcription	NHEK	skin
42	chr1:10590600-10599400	Weak transcription	GM12878-XiMat	blood
43	chr1:10590800-10596200	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr1:10590800-10596400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:10590800-10598600	Weak transcription	Right Atrium	heart
46	chr1:10590800-10599800	Weak transcription	Right Ventricle	heart
47	chr1:10590800-10601000	Weak transcription	A549	lung
48	chr1:10591000-10594600	Weak transcription	Fetal Intestine Small	intestine
49	chr1:10591000-10595800	Weak transcription	Spleen	Spleen
50	chr1:10591000-10596400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links