Variant report

Variant	rs11229130
Chromosome Location	chr11:57562169-57562170
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57542706..57545310-chr11:57561763..57564745,3	MCF-7	breast:
2	chr11:57560773..57562885-chr11:57566656..57568197,2	K562	blood:
3	chr11:57561385..57563451-chr11:57566697..57569615,2	K562	blood:
4	chr11:57529656..57532573-chr11:57561003..57562915,2	MCF-7	breast:
5	chr11:57561542..57564393-chr5:74329604..74332106,2	MCF-7	breast:
6	chr11:57561787..57564365-chr11:57565479..57568145,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198561	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10792112	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896633	0.84[ASN][1000 genomes]
rs10896636	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10896647	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229113	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11229116	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11229131	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229148	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11570190	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11601320	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11601449	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11602109	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11604325	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11604333	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11605731	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11606396	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11607056	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12146541	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12362166	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12785533	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12790196	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12790660	0.84[AFR][1000 genomes]
rs12804972	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12805841	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12807250	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12807357	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1647405	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17455520	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2509808	0.85[EUR][1000 genomes]
rs2847308	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2926656	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35808061	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3781885	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4827	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs488769	0.90[ASN][1000 genomes]
rs499188	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs527528	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs543725	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs547891	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs576859	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs589914	0.85[EUR][1000 genomes]
rs644883	0.83[EUR][1000 genomes]
rs6591434	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs674094	0.81[EUR][1000 genomes]
rs682503	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs708228	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7116341	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7117205	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7117878	0.81[ASN][1000 genomes]
rs7121169	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7129727	0.82[EUR][1000 genomes]
rs71484461	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71484468	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7932091	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7936998	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7938083	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7949841	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9420	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11229130	MED19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57546800-57564000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr11:57555400-57563200	Weak transcription	Fetal Brain Male	brain
3	chr11:57555600-57562800	Weak transcription	Ovary	ovary
4	chr11:57556000-57562400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:57556000-57562400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:57556000-57567800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:57556400-57587800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:57556600-57563000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:57557200-57566200	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr11:57557200-57566200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr11:57558400-57562600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr11:57558400-57567200	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr11:57558400-57567400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr11:57558600-57567200	Strong transcription	Fetal Brain Female	brain
15	chr11:57558800-57563000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:57559400-57571000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr11:57559600-57564000	Weak transcription	Psoas Muscle	Psoas
18	chr11:57559600-57564600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr11:57559800-57562600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr11:57559800-57563000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr11:57559800-57563000	Weak transcription	Right Ventricle	heart
22	chr11:57559800-57566600	Strong transcription	Fetal Stomach	stomach
23	chr11:57559800-57566800	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr11:57560000-57562200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:57560000-57562400	Weak transcription	Brain Germinal Matrix	brain
26	chr11:57560000-57562800	Weak transcription	Fetal Heart	heart
27	chr11:57560000-57563000	Weak transcription	Brain Angular Gyrus	brain
28	chr11:57560000-57563000	Weak transcription	Esophagus	oesophagus
29	chr11:57560000-57563000	Weak transcription	Lung	lung
30	chr11:57560000-57563000	Weak transcription	NHLF	lung
31	chr11:57560000-57563600	Weak transcription	Pancreas	Pancrea
32	chr11:57560000-57564000	Weak transcription	Aorta	Aorta
33	chr11:57560000-57564000	Weak transcription	Gastric	stomach
34	chr11:57560000-57566000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:57560000-57566000	Strong transcription	Left Ventricle	heart
36	chr11:57560200-57563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr11:57560400-57562600	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr11:57560400-57567200	Strong transcription	Fetal Muscle Trunk	muscle
39	chr11:57560600-57563000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr11:57560600-57565000	Strong transcription	HepG2	liver
41	chr11:57560600-57565400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr11:57560600-57566000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr11:57560800-57563000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr11:57560800-57563000	Weak transcription	Thymus	Thymus
45	chr11:57560800-57563200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr11:57560800-57564400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr11:57560800-57564600	Strong transcription	K562	blood
48	chr11:57560800-57566000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr11:57560800-57566000	Strong transcription	NH-A	brain
50	chr11:57561000-57562200	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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