Variant report

Variant	rs3219493
Chromosome Location	chr1:45796269-45796270
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45794537..45798205-chr1:45802201..45806836,5	MCF-7	breast:
2	chr1:45792382..45793922-chr1:45796241..45797777,2	MCF-7	breast:
3	chr1:45195157..45197018-chr1:45796220..45798837,2	K562	blood:
4	chr1:45791057..45793075-chr1:45795554..45797177,2	MCF-7	breast:
5	chr1:45240561..45242696-chr1:45794444..45796919,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186603	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000200169	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12568844	0.80[ASN][1000 genomes]
rs3219479	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3219487	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	esv2750837	chr1:45796115-45908263	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3219493	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs3219493	CCDC163P	cis	Whole Blood	GTEx
rs3219493	CCDC163P	cis	lung	GTEx
rs3219493	CCDC163P	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45787200-45796600	Weak transcription	HepG2	liver
2	chr1:45792400-45800600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:45792800-45804800	Weak transcription	Fetal Kidney	kidney
4	chr1:45792800-45805000	Weak transcription	HSMMtube	muscle
5	chr1:45793000-45796800	Weak transcription	HSMM	muscle
6	chr1:45793200-45796600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:45793200-45796800	Weak transcription	Osteobl	bone
8	chr1:45793200-45797800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:45793200-45804800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:45793400-45796600	Weak transcription	Right Ventricle	heart
11	chr1:45793400-45796800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:45793400-45796800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:45793400-45796800	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:45793400-45803800	Weak transcription	Small Intestine	intestine
15	chr1:45793400-45804000	Weak transcription	HMEC	breast
16	chr1:45793400-45805000	Weak transcription	Right Atrium	heart
17	chr1:45793600-45796600	Weak transcription	Primary B cells from cord blood	blood
18	chr1:45793600-45796600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:45793600-45796800	Weak transcription	Fetal Lung	lung
20	chr1:45793600-45797200	Weak transcription	Left Ventricle	heart
21	chr1:45793600-45797200	Enhancers	Stomach Mucosa	stomach
22	chr1:45793600-45800600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:45793600-45800800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:45793600-45803600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:45793600-45803600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:45793600-45804200	Weak transcription	Fetal Brain Male	brain
27	chr1:45793800-45796800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:45793800-45796800	Weak transcription	Colonic Mucosa	Colon
29	chr1:45793800-45799800	Weak transcription	HUVEC	blood vessel
30	chr1:45793800-45803800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:45794000-45796800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:45794000-45796800	Strong transcription	Spleen	Spleen
33	chr1:45794000-45796800	Weak transcription	NHLF	lung
34	chr1:45794000-45799600	Weak transcription	Fetal Heart	heart
35	chr1:45794000-45800000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr1:45794000-45800200	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:45794000-45800600	Strong transcription	Fetal Stomach	stomach
38	chr1:45794200-45799800	Strong transcription	Fetal Muscle Leg	muscle
39	chr1:45794400-45799600	Strong transcription	Brain Substantia Nigra	brain
40	chr1:45794400-45799800	Strong transcription	Brain Hippocampus Middle	brain
41	chr1:45794400-45799800	Strong transcription	Lung	lung
42	chr1:45794400-45800000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:45794400-45800200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:45794400-45800400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr1:45794400-45800600	Strong transcription	Aorta	Aorta
46	chr1:45794400-45800800	Strong transcription	Fetal Brain Female	brain
47	chr1:45794600-45796600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:45794600-45799600	Strong transcription	Fetal Intestine Small	intestine
49	chr1:45794600-45799600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr1:45794600-45799800	Strong transcription	Fetal Muscle Trunk	muscle

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