Variant report

Variant	rs12223477
Chromosome Location	chr11:76630285-76630286
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:76629872..76631321-chr11:76756709..76758148,6	K562	blood:
2	chr11:76432521..76433371-chr11:76630070..76630907,3	MCF-7	breast:
3	chr11:76517508..76519118-chr11:76629396..76631998,9	MCF-7	breast:
4	chr11:76445248..76448071-chr11:76628717..76631883,4	MCF-7	breast:
5	chr11:76630144..76633520-chr11:76634878..76637709,3	K562	blood:
6	chr11:76573371..76575582-chr11:76628469..76631182,2	MCF-7	breast:
7	chr11:76444256..76445576-chr11:76630135..76631218,4	K562	blood:
8	chr11:76493335..76495613-chr11:76628217..76631203,2	MCF-7	breast:
9	chr11:76498398..76500983-chr11:76629016..76630524,2	MCF-7	breast:
10	chr11:76444662..76445640-chr11:76629853..76630608,2	MCF-7	breast:
11	chr11:76518111..76519175-chr11:76629549..76632027,10	K562	blood:
12	chr11:76630107..76631528-chr11:76750174..76751202,8	MCF-7	breast:
13	chr11:76521037..76521914-chr11:76629597..76630398,3	K562	blood:
14	chr11:76629857..76631654-chr11:76756070..76758105,23	MCF-7	breast:
15	chr11:76570391..76573422-chr11:76629389..76632436,3	MCF-7	breast:
16	chr11:76520927..76521861-chr11:76629465..76631202,7	MCF-7	breast:
17	chr11:76520919..76522194-chr11:76629424..76630709,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000078124	Chromatin interaction
ENSG00000198488	Chromatin interaction
ENSG00000182704	Chromatin interaction
ENSG00000255100	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10899293	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10899314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236997	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11237030	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11602065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11605656	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11606034	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11606467	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1225138	0.82[GIH][hapmap]
rs12797827	0.85[ASN][1000 genomes]
rs17812687	0.81[EUR][1000 genomes]
rs1945084	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1945085	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap]
rs2048954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2187499	0.82[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2279518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2372387	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3740766	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs3740768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4016126	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4944130	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4945128	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs55743360	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55798841	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55977032	0.81[EUR][1000 genomes]
rs56129156	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56789915	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61895512	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61895513	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61900090	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61900119	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61900120	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7115729	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518920	chr11:76573016-76637651	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12223477	GDPD5	cis	parietal	SCAN
rs12223477	ALG8	cis	parietal	SCAN
rs12223477	C2CD3	cis	parietal	SCAN
rs12223477	KLHL35	cis	cerebellum	SCAN
rs12223477	ACER3	cis	lymphoblastoid	seeQTL
rs12223477	CAPN5	cis	parietal	SCAN
rs12223477	ACER3	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76597000-76631000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr11:76613600-76631200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:76615600-76631200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:76618200-76637600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr11:76622600-76631200	Weak transcription	Spleen	Spleen
6	chr11:76622800-76631200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr11:76626600-76631200	Weak transcription	Esophagus	oesophagus
8	chr11:76627400-76631600	Enhancers	K562	blood
9	chr11:76628000-76637600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:76628400-76630800	Weak transcription	Fetal Intestine Small	intestine
11	chr11:76628400-76630800	Weak transcription	HepG2	liver
12	chr11:76629000-76631400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:76629400-76630600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:76629400-76631600	Enhancers	Brain Substantia Nigra	brain
15	chr11:76629800-76630400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr11:76629800-76630400	Enhancers	Fetal Stomach	stomach
17	chr11:76629800-76631400	Enhancers	HUVEC	blood vessel
18	chr11:76629800-76631600	Enhancers	Adipose Nuclei	Adipose
19	chr11:76630000-76630400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr11:76630000-76630400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:76630000-76630400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr11:76630000-76630400	Enhancers	Primary T cells fromperipheralblood	blood
23	chr11:76630000-76630400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:76630000-76630400	Flanking Active TSS	Liver	Liver
25	chr11:76630000-76630400	Active TSS	Brain Anterior Caudate	brain
26	chr11:76630000-76630400	Active TSS	Ovary	ovary
27	chr11:76630000-76630400	Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr11:76630000-76630400	Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr11:76630000-76630400	Flanking Active TSS	A549	lung
30	chr11:76630000-76630400	Active TSS	HSMMtube	muscle
31	chr11:76630000-76630400	Active TSS	NHDF-Ad	bronchial
32	chr11:76630000-76630400	Active TSS	Osteobl	bone
33	chr11:76630000-76630800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr11:76630000-76631000	Enhancers	Primary T cells from cord blood	blood
35	chr11:76630000-76631000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr11:76630000-76631000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr11:76630000-76631000	Enhancers	Fetal Kidney	kidney
38	chr11:76630000-76631000	Enhancers	Hela-S3	cervix
39	chr11:76630000-76631200	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr11:76630000-76631200	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr11:76630000-76631200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr11:76630000-76631200	Weak transcription	HMEC	breast
43	chr11:76630000-76631400	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr11:76630000-76631400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr11:76630000-76631400	Enhancers	Fetal Lung	lung
46	chr11:76630000-76631400	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr11:76630000-76631600	Enhancers	Primary B cells from peripheral blood	blood
48	chr11:76630000-76631600	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr11:76630000-76631600	Enhancers	Brain Hippocampus Middle	brain
50	chr11:76630000-76631600	Enhancers	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links