Variant report

Variant	rs2506884
Chromosome Location	chr1:10579650-10579651
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10578631..10580602-chr1:11071261..11074067,2	MCF-7	breast:
2	chr1:10579090..10582212-chr1:10583289..10585385,3	K562	blood:
3	chr1:10577532..10580475-chr1:10590665..10593408,2	K562	blood:

Variant related genes	Relation type
ENSG00000120948	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12403130	0.82[EUR][1000 genomes]
rs17035156	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2480786	0.90[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2480789	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs2483678	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]
rs2506879	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs2506886	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2506887	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2506888	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs2988399	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61192982	0.85[EUR][1000 genomes]
rs7522072	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2506884	KIF1B	Cis_1M	lymphoblastoid	RTeQTL
rs2506884	PEX14	cis	multi-tissue	Pritchard

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10566800-10579800	Enhancers	Liver	Liver
2	chr1:10570800-10579800	Weak transcription	Aorta	Aorta
3	chr1:10570800-10595600	Weak transcription	Primary B cells from cord blood	blood
4	chr1:10572000-10590000	Weak transcription	Spleen	Spleen
5	chr1:10572200-10598600	Weak transcription	Brain Anterior Caudate	brain
6	chr1:10572600-10587600	Weak transcription	Hela-S3	cervix
7	chr1:10572600-10587800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:10573400-10596000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:10573800-10588000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:10573800-10588200	Weak transcription	Fetal Intestine Large	intestine
11	chr1:10574400-10579800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:10574800-10580600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:10575600-10588000	Weak transcription	NHLF	lung
14	chr1:10576000-10579800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:10576000-10581600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr1:10576000-10589200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr1:10576400-10582000	Weak transcription	Thymus	Thymus
18	chr1:10576400-10582600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:10576400-10582600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:10576400-10596000	Weak transcription	Dnd41	blood
21	chr1:10576600-10579800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:10576600-10579800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr1:10576800-10579800	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr1:10576800-10579800	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr1:10576800-10579800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr1:10576800-10582200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:10577000-10580000	Enhancers	H1 Cell Line	embryonic stem cell
28	chr1:10577000-10603600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:10577200-10582600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:10577200-10584600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:10577400-10580400	Weak transcription	K562	blood
32	chr1:10577400-10580800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:10577400-10582000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr1:10577400-10582000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:10577400-10582200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr1:10577400-10587800	Weak transcription	Pancreas	Pancrea
37	chr1:10577400-10587800	Weak transcription	Right Atrium	heart
38	chr1:10577400-10587800	Weak transcription	HSMM	muscle
39	chr1:10577400-10588000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:10577400-10588000	Weak transcription	Lung	lung
41	chr1:10577400-10588000	Weak transcription	NHDF-Ad	bronchial
42	chr1:10577400-10596400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:10577600-10580000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:10577600-10588000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:10577600-10588400	Weak transcription	Adipose Nuclei	Adipose
46	chr1:10577800-10582400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:10577800-10587800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:10577800-10587800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr1:10577800-10590800	Weak transcription	Fetal Thymus	thymus
50	chr1:10578000-10582000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links