Variant report

Variant	rs2560828
Chromosome Location	chr5:16566212-16566213
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10035580	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10041159	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10053746	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10073468	0.92[ASN][1000 genomes]
rs10454940	0.87[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs12187057	0.81[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs12187879	0.81[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs1551050	0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs2162770	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2617423	0.81[YRI][hapmap]
rs2617426	0.89[YRI][hapmap]
rs56379171	0.92[ASN][1000 genomes]
rs6860945	0.95[CHB][hapmap];0.91[CHD][hapmap];0.80[MEX][hapmap];0.92[ASN][1000 genomes]
rs6862083	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6882868	0.81[CEU][hapmap];0.95[CHB][hapmap];0.92[ASN][1000 genomes]
rs6886993	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7705650	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7730689	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs9312921	0.94[ASN][1000 genomes]
rs9312922	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881187	chr5:16514269-16654960	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2560828	FAM134B	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16522400-16567400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:16542600-16567200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr5:16543200-16591600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr5:16543600-16589800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr5:16545000-16574600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr5:16549200-16569000	Weak transcription	Left Ventricle	heart
7	chr5:16549200-16580200	Weak transcription	Gastric	stomach
8	chr5:16553000-16568600	Weak transcription	NHDF-Ad	bronchial
9	chr5:16553000-16573400	Weak transcription	Fetal Intestine Small	intestine
10	chr5:16553400-16569600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr5:16553400-16572800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr5:16555200-16571400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr5:16556400-16569600	Weak transcription	Primary B cells from cord blood	blood
14	chr5:16556800-16567600	Weak transcription	Fetal Thymus	thymus
15	chr5:16558000-16569000	Weak transcription	Brain Germinal Matrix	brain
16	chr5:16559400-16568200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr5:16559600-16574400	Weak transcription	Fetal Brain Female	brain
18	chr5:16561200-16567200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:16561200-16574400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:16564200-16567000	Enhancers	Fetal Heart	heart
21	chr5:16564400-16566400	Enhancers	Brain Cingulate Gyrus	brain
22	chr5:16564400-16567400	Strong transcription	Primary T cells from cord blood	blood
23	chr5:16564400-16571400	Enhancers	Brain Hippocampus Middle	brain
24	chr5:16564400-16571600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr5:16565000-16567200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr5:16565000-16567400	Weak transcription	Right Atrium	heart
27	chr5:16565000-16567600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr5:16565200-16567000	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr5:16565200-16567400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr5:16565400-16567400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr5:16565400-16569000	Weak transcription	Thymus	Thymus
32	chr5:16565600-16567000	Weak transcription	Brain Anterior Caudate	brain
33	chr5:16565600-16567200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:16565600-16569200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr5:16565600-16573600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr5:16565800-16567000	Weak transcription	Brain Substantia Nigra	brain
37	chr5:16566000-16567000	Weak transcription	Brain Angular Gyrus	brain
38	chr5:16566000-16572800	Weak transcription	Fetal Brain Male	brain
39	chr5:16566000-16580200	Weak transcription	Right Ventricle	heart
40	chr5:16566200-16567000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr5:16566200-16570400	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links