Variant report

Variant	rs5749246
Chromosome Location	chr22:31681062-31681063
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	chr22:31679718..31681431-chr22:31684803..31686641,2	K562	blood:
2	chr22:31680141..31683839-chr22:31741911..31744786,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100105	Chromatin interaction
ENSG00000213888	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1034587	0.95[EUR][1000 genomes]
rs11089491	0.86[EUR][1000 genomes]
rs4618154	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4820961	0.84[AFR][1000 genomes]
rs5749231	0.89[EUR][1000 genomes]
rs5997940	0.95[EUR][1000 genomes]
rs7286926	0.81[AMR][1000 genomes]
rs730286	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067003	chr22:31558663-31697093	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1058844	chr22:31597104-31725296	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5749246	BBS1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31654000-31685600	Strong transcription	Fetal Stomach	stomach
2	chr22:31657800-31681200	Strong transcription	Adipose Nuclei	Adipose
3	chr22:31659000-31685600	Weak transcription	Psoas Muscle	Psoas
4	chr22:31666000-31682600	Strong transcription	Skeletal Muscle Female	skeletal muscle
5	chr22:31666000-31684200	Strong transcription	Aorta	Aorta
6	chr22:31667000-31684600	Weak transcription	Right Atrium	heart
7	chr22:31668400-31681200	Strong transcription	NHLF	lung
8	chr22:31669000-31682200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr22:31669000-31682400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr22:31669000-31685600	Weak transcription	Fetal Brain Male	brain
11	chr22:31669000-31686000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr22:31669200-31682600	Strong transcription	Stomach Smooth Muscle	stomach
13	chr22:31671200-31684600	Weak transcription	Fetal Heart	heart
14	chr22:31671600-31681200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr22:31671800-31686200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr22:31672600-31685600	Strong transcription	Brain Germinal Matrix	brain
17	chr22:31673000-31681800	Strong transcription	Placenta	Placenta
18	chr22:31673800-31685600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr22:31674000-31683800	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr22:31674200-31682600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr22:31674200-31685400	Strong transcription	Fetal Brain Female	brain
22	chr22:31674400-31686400	Weak transcription	Fetal Kidney	kidney
23	chr22:31674400-31686400	Weak transcription	NHDF-Ad	bronchial
24	chr22:31674600-31682600	Strong transcription	Rectal Smooth Muscle	rectum
25	chr22:31675400-31681400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr22:31675400-31682200	Strong transcription	Colon Smooth Muscle	Colon
27	chr22:31675400-31686400	Weak transcription	NH-A	brain
28	chr22:31675800-31681200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
29	chr22:31675800-31685000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr22:31676200-31682200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr22:31676400-31684600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr22:31676600-31681600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr22:31676800-31682200	Weak transcription	GM12878-XiMat	blood
34	chr22:31676800-31682200	Weak transcription	HSMMtube	muscle
35	chr22:31676800-31684800	Weak transcription	Hela-S3	cervix
36	chr22:31676800-31685000	Weak transcription	Osteobl	bone
37	chr22:31677000-31684600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr22:31678000-31686400	Weak transcription	HMEC	breast
39	chr22:31678200-31684000	Strong transcription	Left Ventricle	heart
40	chr22:31678800-31682600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr22:31679000-31685400	Weak transcription	Liver	Liver
42	chr22:31679200-31682200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr22:31679200-31685000	Weak transcription	Fetal Lung	lung
44	chr22:31679200-31685800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr22:31679200-31686400	Weak transcription	HSMM	muscle
46	chr22:31679200-31686600	Weak transcription	Ovary	ovary
47	chr22:31679400-31681600	Genic enhancers	Fetal Intestine Large	intestine
48	chr22:31679400-31682200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr22:31679400-31684800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr22:31679400-31685200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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