Variant report

Variant	rs3765166
Chromosome Location	chr2:172693780-172693781
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	chr2:172692494..172694148-chr2:172705814..172708790,3	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12053046	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12614709	1.00[AFR][1000 genomes];0.98[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];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12620126	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.93[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];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12622895	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12624292	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs17428076	0.89[ASW][hapmap];0.90[CEU][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap]
rs17428174	0.85[CEU][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs17581361	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17581439	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17581481	0.91[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs17581509	0.91[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs17615262	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17615352	0.91[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs2176465	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736499	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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770448	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770449	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770455	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3821093	0.94[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55864623	0.85[EUR][1000 genomes]
rs55957712	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56275355	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57718990	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57775770	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58540694	0.87[ASN][1000 genomes]
rs62182370	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62182372	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62182373	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62182374	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62182392	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6704590	0.85[CEU][hapmap]
rs6761111	0.85[CEU][hapmap]
rs72881938	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72885532	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72885545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72889848	0.87[AMR][1000 genomes]
rs7584258	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
3	nsv1006214	chr2:172691689-172754296	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	nsv536036	chr2:172691689-172754296	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3765166	BBS5	cis	cerebellum	SCAN

Chromatin state (count:117 , 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	chr2:172685600-172694600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr2:172685600-172694800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:172685800-172694000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr2:172686000-172694000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr2:172686200-172698800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:172687000-172694600	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr2:172687200-172694000	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:172687400-172693800	Strong transcription	Brain Anterior Caudate	brain
17	chr2:172687400-172693800	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr2:172687400-172693800	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr2:172687400-172694000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:172687400-172694000	Strong transcription	Brain Cingulate Gyrus	brain
21	chr2:172687400-172694000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:172687400-172694000	Strong transcription	K562	blood
23	chr2:172687600-172693800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:172687600-172693800	Strong transcription	Brain Angular Gyrus	brain
25	chr2:172688000-172693800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:172688400-172693800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:172688400-172694000	Strong transcription	Fetal Thymus	thymus
28	chr2:172688800-172693800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:172688800-172693800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:172689000-172694600	Strong transcription	HUVEC	blood vessel
31	chr2:172689000-172696400	Strong transcription	Primary B cells from peripheral blood	blood
32	chr2:172689400-172693800	Strong transcription	A549	lung
33	chr2:172689400-172693800	Strong transcription	NHLF	lung
34	chr2:172689400-172712200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr2:172689600-172694000	Strong transcription	Brain Germinal Matrix	brain
36	chr2:172689600-172694000	Strong transcription	Fetal Brain Female	brain
37	chr2:172689600-172694000	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:172689600-172695200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr2:172689600-172696600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr2:172689800-172693800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:172689800-172693800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr2:172689800-172693800	Strong transcription	Fetal Muscle Leg	muscle
43	chr2:172689800-172694000	Strong transcription	GM12878-XiMat	blood
44	chr2:172689800-172695200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr2:172689800-172695400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:172689800-172696400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr2:172690000-172694000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:172690000-172694000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:172690000-172694600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:172690000-172694600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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