Variant report

Variant	rs17299006
Chromosome Location	chr1:179939554-179939555
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179939017..179942607-chr1:179944050..179947079,4	K562	blood:
2	chr1:179921069..179927710-chr1:179937007..179944258,10	K562	blood:
3	chr1:179937946..179940776-chr1:179952862..179955374,2	K562	blood:
4	chr1:179923469..179925582-chr1:179939367..179942471,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135837	Chromatin interaction
ENSG00000260360	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10494524	0.84[EUR][1000 genomes]
rs10913920	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12116940	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12118265	1.00[ASN][1000 genomes]
rs12119130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12123201	0.84[EUR][1000 genomes]
rs12123560	0.84[EUR][1000 genomes]
rs12125245	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125592	1.00[ASN][1000 genomes]
rs12126496	1.00[ASN][1000 genomes]
rs12126967	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12127784	1.00[ASN][1000 genomes]
rs12129115	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12130673	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130675	0.84[EUR][1000 genomes]
rs12130720	0.83[EUR][1000 genomes]
rs12131200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132694	0.84[EUR][1000 genomes]
rs12133136	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135751	0.84[EUR][1000 genomes]
rs12136091	1.00[CHB][hapmap]
rs12138429	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12139040	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139323	0.84[EUR][1000 genomes]
rs12139412	0.84[EUR][1000 genomes]
rs12140622	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141134	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141817	0.84[EUR][1000 genomes]
rs12142457	1.00[CHB][hapmap]
rs12144275	0.84[EUR][1000 genomes]
rs12144328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12144346	1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144853	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12145411	0.84[EUR][1000 genomes]
rs12184265	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16855019	0.84[EUR][1000 genomes]
rs16855021	0.84[EUR][1000 genomes]
rs16855022	0.83[EUR][1000 genomes]
rs16855025	0.84[EUR][1000 genomes]
rs16855048	0.81[EUR][1000 genomes]
rs16855049	0.84[EUR][1000 genomes]
rs16855052	0.84[EUR][1000 genomes]
rs16855125	0.82[CEU][hapmap]
rs17371159	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371267	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371308	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1801795	1.00[ASN][1000 genomes]
rs3856048	0.84[EUR][1000 genomes]
rs3856049	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57165548	0.83[EUR][1000 genomes]
rs58463801	0.84[EUR][1000 genomes]
rs61014689	0.84[EUR][1000 genomes]
rs73032352	0.84[EUR][1000 genomes]
rs73039990	0.84[EUR][1000 genomes]
rs73039999	0.84[EUR][1000 genomes]
rs73040001	0.84[EUR][1000 genomes]
rs9701232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9701237	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers 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	48 gene(s)	inside rSNPs	diseases
3	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17299006	CEP350	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179924800-179963600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:179925200-179946200	Weak transcription	Stomach Mucosa	stomach
3	chr1:179925400-179946000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:179925800-179940600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:179926800-179961400	Weak transcription	A549	lung
6	chr1:179927000-179965600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:179927200-179940600	Weak transcription	NHDF-Ad	bronchial
8	chr1:179934600-179945000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:179936000-179946400	Weak transcription	NHLF	lung
10	chr1:179936200-179946000	Weak transcription	Fetal Lung	lung
11	chr1:179936200-179946000	Weak transcription	HepG2	liver
12	chr1:179936400-179955600	Weak transcription	Dnd41	blood
13	chr1:179936600-179958800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:179937200-179941200	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr1:179937400-179941200	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr1:179937600-179939800	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr1:179937600-179939800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:179937600-179939800	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr1:179937600-179941400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:179937600-179941400	Enhancers	Brain Hippocampus Middle	brain
21	chr1:179937800-179939600	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr1:179937800-179939800	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr1:179937800-179940000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr1:179937800-179941400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr1:179937800-179941600	Enhancers	Brain Angular Gyrus	brain
26	chr1:179937800-179941600	Enhancers	Brain Anterior Caudate	brain
27	chr1:179937800-179946200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:179938000-179939800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:179938000-179939800	Enhancers	Colon Smooth Muscle	Colon
30	chr1:179938000-179941200	Enhancers	Brain Substantia Nigra	brain
31	chr1:179938000-179941400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:179938000-179941400	Enhancers	Adipose Nuclei	Adipose
33	chr1:179938000-179983200	Weak transcription	Brain Germinal Matrix	brain
34	chr1:179938200-179939600	Enhancers	Primary hematopoietic stem cells	blood
35	chr1:179938200-179940000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:179938200-179940000	Enhancers	Liver	Liver
37	chr1:179938400-179940000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:179938400-179940000	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr1:179938400-179940000	Enhancers	HSMM	muscle
40	chr1:179938400-179941600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr1:179938400-179943800	Weak transcription	Aorta	Aorta
42	chr1:179938400-179948600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr1:179938600-179940000	Enhancers	Primary T cells from cord blood	blood
44	chr1:179938600-179940000	Enhancers	HUVEC	blood vessel
45	chr1:179938600-179940400	Weak transcription	Ovary	ovary
46	chr1:179938600-179940400	Weak transcription	Pancreas	Pancrea
47	chr1:179938600-179940400	Weak transcription	Spleen	Spleen
48	chr1:179938600-179940400	Weak transcription	K562	blood
49	chr1:179938600-179940600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:179938600-179941200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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