Variant report

Variant	rs540234
Chromosome Location	chr11:57441146-57441147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57439349..57441484-chr11:57580748..57583529,2	MCF-7	breast:
2	chr11:57433015..57436358-chr11:57440099..57444661,8	MCF-7	breast:
3	chr11:57438475..57441494-chr11:57446388..57449628,4	K562	blood:
4	chr11:57439534..57442360-chr11:57509028..57511429,2	K562	blood:
5	chr11:57440494..57443306-chr11:57507739..57511429,4	K562	blood:
6	chr11:57440686..57443520-chr11:57549214..57550745,2	K562	blood:

Variant related genes	Relation type
ENSG00000156599	Chromatin interaction
ENSG00000254732	Chromatin interaction
ENSG00000198561	Chromatin interaction
ENSG00000211450	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10896634	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229087	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11229115	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1267146	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1424752	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2848445	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs479573	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs480933	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs483030	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs486995	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs491719	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs492131	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs501054	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs501738	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs503037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504311	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs504921	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs507946	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs509564	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511708	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs515939	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs517638	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs518804	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs523985	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs527140	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs530094	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs536673	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs537627	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs541245	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs544446	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs549022	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs558653	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs567017	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs577741	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs581217	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58132137	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs594233	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs604094	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs604344	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608648	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs609596	0.87[ASN][1000 genomes]
rs612688	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61888873	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61888880	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs624759	0.86[ASN][1000 genomes]
rs627816	0.82[ASN][1000 genomes]
rs628100	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs636807	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs638864	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs640767	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs645097	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs647264	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs656227	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs658183	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs666021	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs669433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs669950	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs675154	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs676205	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs685110	0.81[ASN][1000 genomes]
rs7108113	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72928102	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs96894	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs540234	MED19	Cis_1M	lymphoblastoid	RTeQTL
rs540234	MED19	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57436600-57479000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:57436800-57441800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:57437400-57442200	Weak transcription	Stomach Mucosa	stomach
4	chr11:57437400-57449800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:57437400-57458000	Weak transcription	Fetal Heart	heart
6	chr11:57437800-57447400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:57438000-57441800	Weak transcription	Psoas Muscle	Psoas
8	chr11:57438000-57442400	Weak transcription	Small Intestine	intestine
9	chr11:57438400-57445400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:57438400-57445800	Strong transcription	Fetal Intestine Large	intestine
11	chr11:57438600-57442200	Genic enhancers	Dnd41	blood
12	chr11:57438600-57443200	Strong transcription	NHLF	lung
13	chr11:57438600-57443600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr11:57438600-57444000	Strong transcription	Duodenum Mucosa	Duodenum
15	chr11:57438600-57464600	Strong transcription	Fetal Brain Female	brain
16	chr11:57438600-57469400	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr11:57438600-57478200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:57438800-57441400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:57438800-57442000	Strong transcription	HMEC	breast
20	chr11:57438800-57444000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr11:57438800-57448000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr11:57438800-57449600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr11:57438800-57464600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr11:57438800-57469600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr11:57438800-57473800	Strong transcription	Fetal Muscle Trunk	muscle
26	chr11:57439000-57441200	Strong transcription	Rectal Smooth Muscle	rectum
27	chr11:57439000-57442000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr11:57439000-57444200	Strong transcription	Primary hematopoietic stem cells	blood
29	chr11:57439000-57445800	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr11:57439000-57447600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:57439000-57469400	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr11:57439000-57473400	Strong transcription	Fetal Thymus	thymus
33	chr11:57439000-57477400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr11:57439200-57441200	Strong transcription	Aorta	Aorta
35	chr11:57439200-57441200	Strong transcription	Colon Smooth Muscle	Colon
36	chr11:57439200-57441400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:57439200-57441600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr11:57439200-57441800	Strong transcription	HepG2	liver
39	chr11:57439200-57442000	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr11:57439200-57442000	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr11:57439200-57442000	Strong transcription	Liver	Liver
42	chr11:57439200-57442600	Strong transcription	Fetal Kidney	kidney
43	chr11:57439200-57443600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr11:57439200-57443800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr11:57439200-57444000	Strong transcription	NH-A	brain
46	chr11:57439200-57445600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr11:57439200-57445600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
48	chr11:57439200-57445800	Strong transcription	Left Ventricle	heart
49	chr11:57439200-57446400	Strong transcription	Adipose Nuclei	Adipose
50	chr11:57439200-57447000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links