Variant report

Variant	rs13130276
Chromosome Location	chr4:175229461-175229462
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:175228750-175230321	K562	blood:	n/a	n/a

Variant related genes	Relation type
CEP44	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10520275	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11939946	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11940726	0.88[ASN][1000 genomes]
rs11940758	0.88[ASN][1000 genomes]
rs11944262	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11946084	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13128257	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17291087	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17291128	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17291408	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34988464	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35918158	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs41279509	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4287982	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695915	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4695919	0.88[ASN][1000 genomes]
rs4695922	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695923	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6553777	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs68084371	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6824643	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6851312	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72702217	0.81[EUR][1000 genomes]
rs7661236	0.88[EUR][1000 genomes]
rs7669484	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016910	chr4:174952788-175349057	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537363	chr4:174952788-175349057	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv596234	chr4:175053051-175361437	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13130276	CEP44	cis	Thyroid	GTEx
rs13130276	KIAA1712	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175205600-175241600	Weak transcription	Small Intestine	intestine
2	chr4:175206000-175235000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:175206200-175241000	Weak transcription	Right Ventricle	heart
4	chr4:175206600-175237800	Weak transcription	Osteobl	bone
5	chr4:175206800-175241800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr4:175207000-175239000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:175207000-175240000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:175207000-175242000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:175214200-175239200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:175214600-175230000	Weak transcription	Fetal Lung	lung
11	chr4:175214600-175230200	Weak transcription	Fetal Brain Male	brain
12	chr4:175214600-175233600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr4:175214600-175236000	Weak transcription	A549	lung
14	chr4:175214600-175237200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr4:175214600-175237400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:175214600-175238000	Weak transcription	HMEC	breast
17	chr4:175214600-175238400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:175214600-175238800	Weak transcription	Aorta	Aorta
19	chr4:175214600-175239000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:175214600-175239000	Weak transcription	HepG2	liver
21	chr4:175214600-175240000	Weak transcription	Colon Smooth Muscle	Colon
22	chr4:175214600-175240200	Weak transcription	Brain Angular Gyrus	brain
23	chr4:175214600-175240600	Weak transcription	Fetal Stomach	stomach
24	chr4:175214600-175241600	Weak transcription	Lung	lung
25	chr4:175214600-175241600	Weak transcription	Thymus	Thymus
26	chr4:175214600-175241800	Weak transcription	Pancreas	Pancrea
27	chr4:175214600-175242000	Weak transcription	Brain Substantia Nigra	brain
28	chr4:175214600-175243200	Weak transcription	Ovary	ovary
29	chr4:175214600-175244800	Weak transcription	Psoas Muscle	Psoas
30	chr4:175214600-175245400	Weak transcription	HSMM	muscle
31	chr4:175214600-175254800	Weak transcription	Esophagus	oesophagus
32	chr4:175214800-175232000	Weak transcription	NHDF-Ad	bronchial
33	chr4:175214800-175239200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr4:175214800-175240000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:175214800-175241200	Weak transcription	Brain Anterior Caudate	brain
36	chr4:175215000-175235800	Weak transcription	Hela-S3	cervix
37	chr4:175215200-175241600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr4:175215200-175242600	Weak transcription	GM12878-XiMat	blood
39	chr4:175217600-175231000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr4:175217600-175232400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr4:175217600-175241600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr4:175217800-175240600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:175218600-175242000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr4:175219000-175239600	Weak transcription	Fetal Brain Female	brain
45	chr4:175219000-175242800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr4:175219400-175233600	Weak transcription	Brain Germinal Matrix	brain
47	chr4:175219400-175235800	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr4:175219600-175235600	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr4:175219600-175237800	Weak transcription	HUVEC	blood vessel
50	chr4:175219800-175233600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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