Variant report

Variant	rs3003888
Chromosome Location	chr1:221982925-221982926
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:221915958..221917862-chr1:221982281..221984311,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs3010845	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4433403	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4451554	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4630135	0.90[ASN][1000 genomes]
rs4846353	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs4846725	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6604672	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7551561	0.89[ASN][1000 genomes]
rs9441867	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription 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	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv873201	chr1:221956626-222007535	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3003888	MOSC1	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221967400-222009800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:221979600-221985000	Enhancers	Primary B cells from peripheral blood	blood
3	chr1:221980000-221984800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:221980200-221984000	Enhancers	Primary hematopoietic stem cells	blood
5	chr1:221981800-221984800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:221982000-221983400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:221982000-221984000	Enhancers	NHEK	skin
8	chr1:221982000-221985000	Enhancers	NHDF-Ad	bronchial
9	chr1:221982200-221983400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr1:221982200-221983400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:221982200-221984200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr1:221982200-221984600	Enhancers	NHLF	lung
13	chr1:221982200-221984800	Enhancers	HMEC	breast
14	chr1:221982400-221983000	Enhancers	Fetal Lung	lung
15	chr1:221982400-221983400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:221982400-221983400	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr1:221982400-221983400	Enhancers	Fetal Thymus	thymus
18	chr1:221982400-221983400	Enhancers	Spleen	Spleen
19	chr1:221982400-221983400	Flanking Active TSS	GM12878-XiMat	blood
20	chr1:221982400-221983600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:221982400-221983800	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr1:221982400-221984200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:221982400-221984200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr1:221982400-221984600	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr1:221982400-221984800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:221982400-221984800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:221982400-221984800	Enhancers	HUVEC	blood vessel
28	chr1:221982400-221984800	Enhancers	NH-A	brain
29	chr1:221982600-221983000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:221982600-221983000	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr1:221982600-221983200	Enhancers	Primary T cells from cord blood	blood
32	chr1:221982600-221983200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr1:221982600-221983400	Enhancers	Primary T cells fromperipheralblood	blood
34	chr1:221982600-221983400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:221982600-221983600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr1:221982600-221984800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:221982800-221983000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr1:221982800-221983400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:221982800-221983400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:221982800-221983600	Weak transcription	Primary B cells from cord blood	blood
41	chr1:221982800-221984200	Weak transcription	Pancreas	Pancrea
42	chr1:221982800-221984800	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links