Variant report

Variant	rs3736499
Chromosome Location	chr2:172690418-172690419
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172684640..172686879-chr2:172687489..172690776,3	K562	blood:
2	chr2:172690324..172692535-chr2:172778951..172781144,3	K562	blood:

Variant related genes	Relation type
ENSG00000128708	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12053046	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12614709	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12619041	0.95[CEU][hapmap];0.83[CHB][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12620126	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12622385	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs12622772	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12622895	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12624292	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs17428076	0.90[CEU][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs17428174	0.84[CEU][hapmap];0.91[TSI][hapmap]
rs17581361	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17581439	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17581481	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs17581509	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs17615262	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17615352	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2176465	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3765166	0.89[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765167	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770448	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770455	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3821093	0.94[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55864623	0.83[EUR][1000 genomes]
rs55957712	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56275355	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57718990	0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs57775770	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58540694	0.87[ASN][1000 genomes]
rs62182370	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62182372	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62182373	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62182374	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62182392	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6704590	0.84[CEU][hapmap]
rs6761111	0.84[CEU][hapmap]
rs72881938	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72885532	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72885545	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72889848	0.89[AMR][1000 genomes]
rs7584258	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[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	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv583611	chr2:172683481-172750257	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3736499	BBS5	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172681000-172695000	Weak transcription	Pancreas	Pancrea
2	chr2:172681800-172693800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr2:172682000-172694000	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr2:172683400-172693800	Strong transcription	Stomach Smooth Muscle	stomach
5	chr2:172683400-172694400	Strong transcription	Primary T cells from cord blood	blood
6	chr2:172683600-172693800	Strong transcription	Left Ventricle	heart
7	chr2:172683800-172694200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:172684400-172694000	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr2:172684600-172691600	Strong transcription	Ovary	ovary
10	chr2:172685000-172691200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
11	chr2:172685200-172691600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
12	chr2:172685400-172691600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
13	chr2:172685600-172693000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:172685600-172694600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr2:172685600-172694800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:172685800-172691400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
17	chr2:172685800-172694000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr2:172686000-172694000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr2:172686200-172691800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
20	chr2:172686200-172698800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:172686800-172693600	Strong transcription	Colon Smooth Muscle	Colon
22	chr2:172687000-172694600	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr2:172687200-172690600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:172687200-172690600	Weak transcription	Liver	Liver
25	chr2:172687200-172692200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:172687200-172693600	Strong transcription	Rectal Smooth Muscle	rectum
27	chr2:172687200-172694000	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:172687400-172691200	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
29	chr2:172687400-172691200	ZNF genes & repeats	Dnd41	blood
30	chr2:172687400-172691400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
31	chr2:172687400-172691600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:172687400-172691600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:172687400-172691800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:172687400-172693200	Strong transcription	Colonic Mucosa	Colon
35	chr2:172687400-172693400	Strong transcription	HSMMtube	muscle
36	chr2:172687400-172693800	Strong transcription	Brain Anterior Caudate	brain
37	chr2:172687400-172693800	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr2:172687400-172693800	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr2:172687400-172694000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:172687400-172694000	Strong transcription	Brain Cingulate Gyrus	brain
41	chr2:172687400-172694000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:172687400-172694000	Strong transcription	K562	blood
43	chr2:172687600-172693400	Strong transcription	Brain Hippocampus Middle	brain
44	chr2:172687600-172693600	Strong transcription	Adipose Nuclei	Adipose
45	chr2:172687600-172693800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:172687600-172693800	Strong transcription	Brain Angular Gyrus	brain
47	chr2:172687800-172690600	Strong transcription	Hela-S3	cervix
48	chr2:172688000-172693800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:172688200-172691400	Strong transcription	Fetal Intestine Large	intestine
50	chr2:172688400-172691400	Strong transcription	Esophagus	oesophagus

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