Variant report

Variant	rs12223479
Chromosome Location	chr11:66290065-66290066
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66286543..66288664-chr11:66289775..66291929,2	MCF-7	breast:
2	chr11:66280554..66282642-chr11:66287328..66290306,2	MCF-7	breast:
3	chr11:66280233..66283147-chr11:66288222..66290856,2	K562	blood:

Variant related genes	Relation type
ENSG00000174483	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10501397	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10896124	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10896125	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10896129	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11227495	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11227497	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11227498	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11227499	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11227500	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11227501	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11227502	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11227503	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11227506	0.83[ASN][1000 genomes]
rs11227509	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11227510	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11227511	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11227512	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11227514	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11227515	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11227522	0.90[AMR][1000 genomes]
rs11227523	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11227525	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11227527	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11227534	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11550299	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11821155	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11822028	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11822099	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11824771	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12099041	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12221821	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12272545	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17065	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17147644	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17496250	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17496586	0.85[EUR][1000 genomes]
rs2075792	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2276406	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2277302	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2279864	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2298806	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305532	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305533	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305534	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2305535	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28414721	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3179961	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35733139	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3737525	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3741360	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3816492	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3819247	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3825065	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3892818	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4542420	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4576	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4630309	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4930183	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4930377	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4930378	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4930379	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4930380	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56144989	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57045447	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57207756	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57288351	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57596493	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57634456	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57691879	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57724777	0.84[EUR][1000 genomes]
rs59829960	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59982644	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60358007	0.81[EUR][1000 genomes]
rs60645853	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61561111	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61582507	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7116921	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7116940	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7123176	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7928882	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7939759	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7943327	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7950407	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7950790	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
2	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv468601	chr11:66234023-66296114	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv555224	chr11:66234023-66296114	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12223479	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs12223479	DPP3	cis	Thyroid	GTEx
rs12223479	CTD-3074O7.12	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66278600-66311000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:66278800-66290400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:66278800-66290600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:66278800-66294000	Weak transcription	Aorta	Aorta
5	chr11:66278800-66309800	Weak transcription	HSMMtube	muscle
6	chr11:66278800-66312800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:66279000-66290200	Weak transcription	HMEC	breast
8	chr11:66279000-66291200	Weak transcription	Psoas Muscle	Psoas
9	chr11:66279000-66303000	Weak transcription	Primary B cells from cord blood	blood
10	chr11:66279000-66306200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:66279000-66309200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr11:66279000-66313000	Weak transcription	Small Intestine	intestine
13	chr11:66279200-66290600	Weak transcription	Fetal Heart	heart
14	chr11:66279200-66295400	Weak transcription	Fetal Kidney	kidney
15	chr11:66279200-66309800	Weak transcription	HUVEC	blood vessel
16	chr11:66279200-66310400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr11:66279200-66310800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr11:66279200-66310800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr11:66279400-66295000	Weak transcription	K562	blood
20	chr11:66279400-66311000	Weak transcription	Fetal Brain Male	brain
21	chr11:66279400-66311200	Weak transcription	Right Atrium	heart
22	chr11:66279800-66305200	Strong transcription	Fetal Muscle Leg	muscle
23	chr11:66280000-66292400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr11:66280400-66292000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:66280600-66291800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr11:66281000-66292000	Strong transcription	Fetal Intestine Small	intestine
27	chr11:66281000-66311000	Strong transcription	Fetal Stomach	stomach
28	chr11:66281400-66292200	Strong transcription	Fetal Muscle Trunk	muscle
29	chr11:66282000-66309600	Weak transcription	NHDF-Ad	bronchial
30	chr11:66283000-66290400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:66283200-66290600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr11:66283400-66312800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr11:66283600-66290200	Weak transcription	NH-A	brain
34	chr11:66285400-66291600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:66285400-66292000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr11:66285400-66292600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr11:66285600-66292000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:66285600-66292000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr11:66285600-66292200	Strong transcription	Stomach Smooth Muscle	stomach
40	chr11:66285800-66291400	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr11:66286000-66291600	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr11:66286200-66291400	Strong transcription	Osteobl	bone
43	chr11:66286200-66292000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr11:66286200-66292000	Strong transcription	Fetal Intestine Large	intestine
45	chr11:66286200-66292200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:66286200-66292200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:66286200-66301000	Strong transcription	Placenta	Placenta
48	chr11:66286200-66301200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr11:66286400-66290800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:66286400-66291600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links