Variant report

Variant	rs11231183
Chromosome Location	chr11:62442621-62442622
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:62441950-62442622	GM12892	blood:	n/a	n/a
2	POLR2A	chr11:62438051-62443358	HepG2	liver:	n/a	n/a
3	POLR2A	chr11:62441880-62442625	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr11:62442389-62443301	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:62436186..62443328-chr11:62605173..62609692,11	MCF-7	breast:
2	chr11:62442193..62444955-chr11:62459578..62462462,2	MCF-7	breast:
3	chr11:62355264..62375429-chr11:62428418..62443271,77	MCF-7	breast:
4	chr11:62436333..62448417-chr11:62605662..62610542,19	K562	blood:

Variant related genes	Relation type
C11orf48	TF binding region
ENSG00000255508	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000149499	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000168000	Chromatin interaction
ENSG00000149480	Chromatin interaction
ENSG00000254964	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10792355	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10792356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10897289	0.92[ASN][1000 genomes]
rs11231172	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11231173	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11231176	0.93[EUR][1000 genomes]
rs11231181	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11231182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231184	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12291465	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12364753	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12364756	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13941	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17637597	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1893458	0.97[ASN][1000 genomes]
rs2956993	0.97[ASN][1000 genomes]
rs2956995	0.97[ASN][1000 genomes]
rs2957122	0.88[ASN][1000 genomes]
rs2958236	0.88[ASN][1000 genomes]
rs3017188	0.90[ASN][1000 genomes]
rs3017666	0.82[ASN][1000 genomes]
rs3809079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4489748	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs489778	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597259	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60435036	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs661182	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67909703	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs693698	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128852	0.81[ASN][1000 genomes]
rs71490396	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71490397	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7949030	0.92[ASN][1000 genomes]
rs9736354	0.84[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	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1401 gene(s)	inside rSNPs	diseases
4	nsv832182	chr11:62295575-62462848	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
5	nsv497903	chr11:62330308-62608042	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	489 gene(s)	inside rSNPs	diseases
6	nsv555174	chr11:62334096-62496519	Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	243 gene(s)	inside rSNPs	diseases
7	nsv897623	chr11:62438819-62603916	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	215 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11231183	B3GAT3	cis	Esophagus Muscularis	GTEx
rs11231183	EML3	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62439800-62445800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:62440000-62443800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:62440000-62443800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:62440000-62443800	Weak transcription	Aorta	Aorta
5	chr11:62440000-62443800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr11:62440000-62444000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:62440000-62444000	Weak transcription	Ovary	ovary
8	chr11:62440000-62445400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr11:62440000-62445600	Weak transcription	Fetal Kidney	kidney
10	chr11:62440200-62443800	Weak transcription	Psoas Muscle	Psoas
11	chr11:62440200-62445000	Weak transcription	Right Atrium	heart
12	chr11:62440200-62445600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr11:62440400-62444800	Weak transcription	Stomach Mucosa	stomach
14	chr11:62440400-62445000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:62440400-62445200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:62440600-62442800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:62440600-62442800	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr11:62440600-62443200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr11:62440600-62443800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr11:62440600-62443800	Weak transcription	Primary T cells from cord blood	blood
21	chr11:62440600-62443800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr11:62440600-62443800	Weak transcription	Fetal Brain Female	brain
23	chr11:62440600-62443800	Weak transcription	Spleen	Spleen
24	chr11:62440600-62443800	Weak transcription	HSMM	muscle
25	chr11:62440600-62444200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr11:62440600-62444200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr11:62440600-62444200	Strong transcription	Fetal Muscle Trunk	muscle
28	chr11:62440600-62444600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr11:62440600-62445200	Strong transcription	Brain Anterior Caudate	brain
30	chr11:62440600-62445200	Strong transcription	Fetal Stomach	stomach
31	chr11:62440600-62445400	Strong transcription	Lung	lung
32	chr11:62440800-62443000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr11:62440800-62443800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr11:62440800-62443800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr11:62440800-62443800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr11:62440800-62443800	Weak transcription	Esophagus	oesophagus
37	chr11:62440800-62443800	Weak transcription	Gastric	stomach
38	chr11:62440800-62444000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr11:62440800-62444000	Weak transcription	Colonic Mucosa	Colon
40	chr11:62440800-62444200	Weak transcription	Brain Angular Gyrus	brain
41	chr11:62440800-62444600	Weak transcription	HMEC	breast
42	chr11:62440800-62444800	Strong transcription	Left Ventricle	heart
43	chr11:62440800-62445000	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr11:62440800-62445000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr11:62440800-62445000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr11:62440800-62445400	Weak transcription	Small Intestine	intestine
47	chr11:62440800-62445600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr11:62441000-62443200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:62441000-62443200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:62441000-62443800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links