Variant report

Variant	rs12224672
Chromosome Location	chr11:47500400-47500401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47497888..47500480-chr11:47502377..47505310,2	K562	blood:
2	chr11:47492716..47498082-chr11:47498479..47503693,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149187	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10838703	0.86[AMR][1000 genomes]
rs11039266	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11039284	0.83[AMR][1000 genomes]
rs12361415	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280231	0.83[AMR][1000 genomes]
rs61895112	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7103835	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7933019	0.81[AFR][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	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12224672	FNBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:132 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47480000-47510000	Strong transcription	Thymus	Thymus
2	chr11:47480600-47508400	Strong transcription	Fetal Intestine Small	intestine
3	chr11:47480800-47511000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:47480800-47511400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr11:47483400-47508800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr11:47483600-47511400	Strong transcription	Dnd41	blood
7	chr11:47484800-47504800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr11:47484800-47510600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr11:47484800-47511000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr11:47485200-47511400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr11:47485400-47504800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr11:47485400-47511400	Strong transcription	Primary B cells from cord blood	blood
13	chr11:47485600-47511000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr11:47485800-47518200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr11:47486000-47510000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr11:47486200-47511200	Strong transcription	Primary B cells from peripheral blood	blood
17	chr11:47486200-47511200	Strong transcription	Primary T cells from cord blood	blood
18	chr11:47486400-47510200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr11:47487800-47507400	Strong transcription	Fetal Intestine Large	intestine
20	chr11:47488200-47510800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr11:47488200-47511200	Strong transcription	GM12878-XiMat	blood
22	chr11:47488400-47509000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr11:47488400-47509800	Strong transcription	Placenta	Placenta
24	chr11:47488800-47510800	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr11:47489000-47501000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
26	chr11:47489200-47500800	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr11:47489200-47508400	Strong transcription	Fetal Stomach	stomach
28	chr11:47489200-47508800	Strong transcription	Spleen	Spleen
29	chr11:47489200-47510800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr11:47489200-47522800	Strong transcription	Fetal Thymus	thymus
31	chr11:47489400-47510800	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr11:47489800-47509200	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr11:47489800-47510000	Strong transcription	Duodenum Mucosa	Duodenum
34	chr11:47489800-47510600	Strong transcription	Fetal Muscle Trunk	muscle
35	chr11:47490000-47509000	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr11:47490000-47510600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr11:47490000-47511000	Strong transcription	Primary hematopoietic stem cells	blood
38	chr11:47490600-47500600	Strong transcription	Pancreas	Pancrea
39	chr11:47490600-47508800	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr11:47490600-47509400	Strong transcription	Fetal Lung	lung
41	chr11:47490800-47501000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr11:47490800-47510800	Strong transcription	HSMMtube	muscle
43	chr11:47491000-47507200	Strong transcription	Colonic Mucosa	Colon
44	chr11:47491000-47509000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr11:47491200-47500400	Strong transcription	Left Ventricle	heart
46	chr11:47491200-47508800	Strong transcription	Fetal Brain Female	brain
47	chr11:47491400-47500600	Strong transcription	Aorta	Aorta
48	chr11:47491400-47500600	Strong transcription	Right Ventricle	heart
49	chr11:47491400-47510600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:47491400-47510600	Strong transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links