Variant report

Variant	rs2483678
Chromosome Location	chr1:10582047-10582048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10581501..10583988-chr1:10587081..10589695,2	MCF-7	breast:
2	chr1:10579090..10582212-chr1:10583289..10585385,3	K562	blood:
3	chr1:10575137..10577327-chr1:10580431..10584030,4	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10157111	0.88[GIH][hapmap]
rs10864463	0.88[GIH][hapmap]
rs12403130	0.82[EUR][1000 genomes]
rs17035156	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2480772	0.95[GIH][hapmap]
rs2480773	0.95[GIH][hapmap]
rs2480775	0.95[GIH][hapmap]
rs2480780	0.81[YRI][hapmap]
rs2480786	0.86[ASW][hapmap];0.90[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2480789	1.00[CEU][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs2506878	0.95[GIH][hapmap];0.82[TSI][hapmap]
rs2506879	0.90[CEU][hapmap]
rs2506884	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2506886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2506887	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2506888	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs2506898	0.95[GIH][hapmap]
rs2988399	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4240915	0.88[GIH][hapmap]
rs4846228	0.84[TSI][hapmap]
rs4846230	0.95[GIH][hapmap]
rs61192982	0.85[EUR][1000 genomes]
rs7512467	0.90[GIH][hapmap]
rs7522072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs944191	0.93[GIH][hapmap]
rs9660006	0.88[GIH][hapmap]
rs9970001	0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2483678	APITD1	cis	cerebellum	SCAN
rs2483678	PEX14	cis	multi-tissue	Pritchard
rs2483678	VAMP3	cis	parietal	SCAN
rs2483678	PEX14	cis	Lymphoblastoid	GTEx
rs2483678	KIF1B	cis	multi-tissue	Pritchard

Chromatin state (count:101 , 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	chr1:10572000-10590000	Weak transcription	Spleen	Spleen
3	chr1:10572200-10598600	Weak transcription	Brain Anterior Caudate	brain
4	chr1:10572600-10587600	Weak transcription	Hela-S3	cervix
5	chr1:10572600-10587800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:10573400-10596000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:10573800-10588000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:10573800-10588200	Weak transcription	Fetal Intestine Large	intestine
9	chr1:10575600-10588000	Weak transcription	NHLF	lung
10	chr1:10576000-10589200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr1:10576400-10582600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:10576400-10582600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:10576400-10596000	Weak transcription	Dnd41	blood
14	chr1:10576800-10582200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:10577000-10603600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:10577200-10582600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr1:10577200-10584600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:10577400-10582200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:10577400-10587800	Weak transcription	Pancreas	Pancrea
20	chr1:10577400-10587800	Weak transcription	Right Atrium	heart
21	chr1:10577400-10587800	Weak transcription	HSMM	muscle
22	chr1:10577400-10588000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:10577400-10588000	Weak transcription	Lung	lung
24	chr1:10577400-10588000	Weak transcription	NHDF-Ad	bronchial
25	chr1:10577400-10596400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:10577600-10588000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:10577600-10588400	Weak transcription	Adipose Nuclei	Adipose
28	chr1:10577800-10582400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:10577800-10587800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:10577800-10587800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:10577800-10590800	Weak transcription	Fetal Thymus	thymus
32	chr1:10578000-10582400	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr1:10578000-10587800	Weak transcription	HMEC	breast
34	chr1:10578000-10588000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:10578200-10587800	Weak transcription	NHEK	skin
36	chr1:10578200-10588400	Weak transcription	Fetal Kidney	kidney
37	chr1:10578200-10589800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:10578400-10590600	Weak transcription	Placenta	Placenta
39	chr1:10579200-10582200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr1:10579200-10582400	Weak transcription	Fetal Muscle Leg	muscle
41	chr1:10579400-10582600	Weak transcription	Fetal Brain Male	brain
42	chr1:10579400-10583800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:10579400-10589200	Weak transcription	Gastric	stomach
44	chr1:10579400-10610200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:10579600-10582200	Weak transcription	Fetal Lung	lung
46	chr1:10579600-10587800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:10579600-10587800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:10579600-10587800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:10579600-10587800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr1:10579600-10587800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links