Variant report

Variant	rs12225316
Chromosome Location	chr11:67976003-67976004
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:67969934..67972866-chr11:67975258..67976822,2	K562	blood:
2	chr11:67887694..67890198-chr11:67975393..67978170,3	MCF-7	breast:
3	chr11:67969945..67972866-chr11:67975145..67976832,3	K562	blood:
4	chr11:67971319..67974316-chr11:67975628..67978548,2	MCF-7	breast:
5	chr11:67878032..67880524-chr11:67975715..67978207,2	MCF-7	breast:
6	chr11:67963420..67968782-chr11:67971477..67978246,6	MCF-7	breast:
7	chr11:67783191..67785391-chr11:67975759..67978285,2	K562	blood:
8	chr11:67887687..67889876-chr11:67974814..67978296,4	MCF-7	breast:
9	chr11:67802935..67805525-chr11:67975520..67978428,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000110717	Chromatin interaction
ENSG00000110721	Chromatin interaction
ENSG00000255236	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10896298	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10896301	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896304	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10896305	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1894204	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2011157	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2054865	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34236202	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34493482	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4345973	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4930228	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4930229	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4930230	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4930561	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4930563	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4930564	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61890513	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7950452	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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	nsv825963	chr11:67763676-68197054	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	esv3347272	chr11:67969427-68218997	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12225316	SUV420H1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67952600-67977000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:67953000-67976800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:67953800-67978600	Weak transcription	Aorta	Aorta
4	chr11:67954000-67976200	Weak transcription	Placenta	Placenta
5	chr11:67954200-67976800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr11:67954400-67976800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:67954600-67976600	Weak transcription	Thymus	Thymus
8	chr11:67956400-67978600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr11:67957600-67976200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr11:67957600-67976400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr11:67959200-67976400	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr11:67960200-67976400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:67960800-67976800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr11:67966200-67976400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr11:67966200-67976600	Weak transcription	NHEK	skin
16	chr11:67968200-67977000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:67968400-67976800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:67968800-67976400	Weak transcription	Osteobl	bone
19	chr11:67969000-67976800	Weak transcription	NHDF-Ad	bronchial
20	chr11:67969000-67979200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:67970000-67976400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr11:67971600-67976200	Weak transcription	Fetal Kidney	kidney
23	chr11:67971600-67976800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr11:67971800-67976800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr11:67972000-67976200	Weak transcription	Fetal Brain Female	brain
26	chr11:67972000-67976400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr11:67972000-67976400	Weak transcription	Fetal Thymus	thymus
28	chr11:67972000-67976600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr11:67972000-67976800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr11:67972000-67976800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr11:67972000-67976800	Weak transcription	Spleen	Spleen
32	chr11:67972200-67976400	Weak transcription	Lung	lung
33	chr11:67972400-67976400	Weak transcription	Right Atrium	heart
34	chr11:67972400-67976800	Weak transcription	Esophagus	oesophagus
35	chr11:67972800-67976200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr11:67973400-67976800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr11:67973400-67979000	Enhancers	Liver	Liver
38	chr11:67974000-67976200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr11:67974000-67976200	Weak transcription	Hela-S3	cervix
40	chr11:67974000-67976400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr11:67974000-67976400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr11:67974000-67976600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr11:67974000-67976600	Weak transcription	GM12878-XiMat	blood
44	chr11:67974000-67976800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr11:67974000-67976800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr11:67974000-67976800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr11:67974000-67976800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr11:67974000-67978200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:67974000-67978200	Weak transcription	Small Intestine	intestine
50	chr11:67974200-67976200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links