Variant report

Variant	rs11168822
Chromosome Location	chr12:49405743-49405744
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49349323..49352262-chr12:49403962..49406098,2	MCF-7	breast:
2	chr12:49389429..49391969-chr12:49402571..49406442,3	MCF-7	breast:
3	chr12:49402719..49406068-chr12:49407016..49408969,3	MCF-7	breast:
4	chr12:49404764..49408231-chr12:49523736..49525425,3	K562	blood:

Variant related genes	Relation type
ENSG00000134287	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000272822	Chromatin interaction
ENSG00000123416	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1054442	0.94[ASN][1000 genomes]
rs10747559	0.83[ASN][1000 genomes]
rs10783299	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10783300	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783301	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10875906	0.92[ASN][1000 genomes]
rs10875908	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875910	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875911	0.97[ASN][1000 genomes]
rs10875912	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10875913	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875914	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875915	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168827	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168838	0.81[ASN][1000 genomes]
rs11168839	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1138908	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11614738	0.93[ASN][1000 genomes]
rs12580349	0.83[ASN][1000 genomes]
rs2117029	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241726	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2293445	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2293446	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304275	0.85[ASN][1000 genomes]
rs34436857	0.87[ASN][1000 genomes]
rs3741619	0.92[ASN][1000 genomes]
rs3741622	0.85[ASN][1000 genomes]
rs3782357	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7969091	0.82[ASN][1000 genomes]
rs876333	0.93[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	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
4	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11168822	RP11-386G11.3	cis	Muscle Skeletal	GTEx
rs11168822	DDN	cis	Muscle Skeletal	GTEx
rs11168822	RP11-386G11.5	cis	Muscle Skeletal	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49395400-49407000	Strong transcription	Primary B cells from peripheral blood	blood
2	chr12:49395400-49407200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:49395400-49411600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:49395600-49407600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr12:49396000-49411600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:49396600-49407600	Weak transcription	Fetal Heart	heart
7	chr12:49396800-49411400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:49397000-49411200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:49397000-49411400	Weak transcription	Fetal Brain Male	brain
10	chr12:49397200-49411600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr12:49397600-49411400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:49399200-49411400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:49399600-49405800	Weak transcription	Esophagus	oesophagus
14	chr12:49399600-49406000	Weak transcription	Small Intestine	intestine
15	chr12:49399600-49407200	Weak transcription	K562	blood
16	chr12:49399600-49411000	Weak transcription	Pancreas	Pancrea
17	chr12:49399800-49406400	Weak transcription	Brain Angular Gyrus	brain
18	chr12:49399800-49411000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr12:49399800-49411400	Weak transcription	Fetal Kidney	kidney
20	chr12:49399800-49411600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:49400000-49410200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:49401200-49407400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr12:49401400-49407400	Strong transcription	Primary T cells from cord blood	blood
24	chr12:49401600-49407200	Strong transcription	Fetal Stomach	stomach
25	chr12:49401800-49407000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr12:49401800-49407600	Strong transcription	Osteobl	bone
27	chr12:49402000-49406800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:49402000-49407000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:49402000-49407200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:49402000-49407200	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:49402000-49407400	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:49402000-49407600	Strong transcription	Dnd41	blood
33	chr12:49402200-49406800	Strong transcription	Primary B cells from cord blood	blood
34	chr12:49402200-49407000	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr12:49402200-49407000	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr12:49402200-49407000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:49402200-49407000	Strong transcription	Colon Smooth Muscle	Colon
38	chr12:49402200-49407000	Strong transcription	Fetal Thymus	thymus
39	chr12:49402200-49407000	Strong transcription	NH-A	brain
40	chr12:49402200-49407200	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr12:49402200-49407200	Strong transcription	Fetal Muscle Leg	muscle
42	chr12:49402200-49407200	Strong transcription	Stomach Smooth Muscle	stomach
43	chr12:49402200-49407400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:49402400-49407000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr12:49402600-49407000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:49402600-49407000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:49402600-49408400	Weak transcription	Psoas Muscle	Psoas
48	chr12:49403000-49406000	Weak transcription	Hela-S3	cervix
49	chr12:49403000-49407000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:49403000-49407200	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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