Variant report

Variant	rs2317132
Chromosome Location	chr3:56645706-56645707
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10222629	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1054092	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1054093	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11130525	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130526	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130527	0.97[EUR][1000 genomes]
rs11712664	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11712799	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11719707	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11719726	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1316647	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13317989	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1388256	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565378	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17216685	0.88[ASN][1000 genomes]
rs17216747	0.83[ASN][1000 genomes]
rs17288852	0.87[ASN][1000 genomes]
rs1812347	0.97[EUR][1000 genomes]
rs1873256	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2291498	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2291500	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs282525	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282530	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282531	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282542	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3172355	0.95[ASN][1000 genomes]
rs3732505	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4681726	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4681736	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4681738	0.82[ASN][1000 genomes]
rs4681903	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4681904	0.96[ASN][1000 genomes]
rs4681937	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4681955	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682001	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4682002	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4974221	0.87[ASN][1000 genomes]
rs4974223	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4974225	0.92[EUR][1000 genomes]
rs55742226	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55828519	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55865922	0.81[ASN][1000 genomes]
rs56126040	0.81[ASN][1000 genomes]
rs56172256	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56263252	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56356916	0.87[ASN][1000 genomes]
rs62251234	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62255964	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6445811	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6445812	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6556	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6764730	0.97[EUR][1000 genomes]
rs6767903	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6794450	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6799086	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7612464	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7620896	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7628343	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7633478	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7641898	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7645941	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7647095	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7648297	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7649872	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs873840	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9311609	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9311612	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs953540	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9809117	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9809741	0.82[EUR][1000 genomes]
rs9816100	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9816265	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9819952	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9826788	0.94[ASN][1000 genomes]
rs9830377	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9834239	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9835134	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9841851	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9847362	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9861577	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9864701	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9867302	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9868059	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9871265	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9872059	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9881152	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9883842	0.86[EUR][1000 genomes];0.95[ASN][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	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2317132	CCDC66	Cis_1M	lymphoblastoid	RTeQTL
rs2317132	CCDC66	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56603200-56650400	Weak transcription	K562	blood
2	chr3:56606200-56650200	Weak transcription	Colonic Mucosa	Colon
3	chr3:56607800-56650200	Weak transcription	Psoas Muscle	Psoas
4	chr3:56625200-56650400	Weak transcription	NHEK	skin
5	chr3:56625200-56653400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:56626400-56656200	Weak transcription	Stomach Mucosa	stomach
7	chr3:56628600-56649600	Weak transcription	HepG2	liver
8	chr3:56629000-56647400	Weak transcription	HUVEC	blood vessel
9	chr3:56629000-56648000	Weak transcription	NH-A	brain
10	chr3:56629600-56648200	Weak transcription	NHDF-Ad	bronchial
11	chr3:56630000-56654400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:56630600-56645800	Weak transcription	HSMM	muscle
13	chr3:56633800-56647800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:56634000-56651400	Weak transcription	Fetal Brain Male	brain
15	chr3:56640000-56650000	Weak transcription	HMEC	breast
16	chr3:56640400-56650800	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:56640600-56646800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:56640600-56647200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:56640600-56647600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:56640600-56647800	Weak transcription	GM12878-XiMat	blood
21	chr3:56640600-56650400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:56640600-56652600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:56640800-56645800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:56640800-56646000	Weak transcription	Spleen	Spleen
25	chr3:56640800-56646200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:56640800-56646400	Weak transcription	Esophagus	oesophagus
27	chr3:56640800-56646400	Weak transcription	Gastric	stomach
28	chr3:56640800-56646600	Weak transcription	Aorta	Aorta
29	chr3:56640800-56646800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:56640800-56647000	Weak transcription	Liver	Liver
31	chr3:56640800-56647200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr3:56640800-56647400	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr3:56640800-56647400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:56640800-56647400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr3:56640800-56647600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:56640800-56647600	Weak transcription	Brain Angular Gyrus	brain
37	chr3:56640800-56647800	Weak transcription	Dnd41	blood
38	chr3:56640800-56649400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:56640800-56649400	Weak transcription	Osteobl	bone
40	chr3:56640800-56649800	Weak transcription	Fetal Kidney	kidney
41	chr3:56640800-56650400	Weak transcription	NHLF	lung
42	chr3:56640800-56650600	Weak transcription	HSMMtube	muscle
43	chr3:56640800-56650800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:56640800-56664200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:56640800-56695400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:56641200-56647000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:56641200-56647000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr3:56641400-56646200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:56642800-56713400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr3:56643000-56649400	Strong transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links