Variant report

Variant	rs11123139
Chromosome Location	chr2:113305150-113305151
allele	C/G
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	STAT3	chr2:113304945-113305203	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr2:113304913-113305232	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr2:113304941-113305312	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr2:113304934-113305247	A549	lung:	n/a	chr2:113305069-113305080
5	FOS	chr2:113304944-113305203	MCF10A-Er-Src	breast:	n/a	n/a
6	MYC	chr2:113304913-113305322	MCF10A-Er-Src	breast:	n/a	n/a
7	CEBPB	chr2:113304997-113305169	HepG2	liver:	n/a	chr2:113305069-113305080
8	STAT3	chr2:113304984-113305227	MCF10A-Er-Src	breast:	n/a	n/a
9	CEBPB	chr2:113304910-113305297	ECC-1	luminal epithelium:	n/a	chr2:113305069-113305080
10	CEBPB	chr2:113304939-113305270	HepG2	liver:	n/a	chr2:113305069-113305080
11	FOS	chr2:113304937-113305241	MCF10A-Er-Src	breast:	n/a	n/a
12	MYC	chr2:113304886-113305346	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr2:113304913-113305242	MCF10A-Er-Src	breast:	n/a	n/a
14	MAX	chr2:113304902-113305362	ECC-1	luminal epithelium:	n/a	n/a
15	CEBPB	chr2:113304905-113305288	Hela-S3	cervix:	n/a	chr2:113305069-113305080
16	ZNF263	chr2:113304898-113305310	HEK293-T-REx	kidney:	n/a	n/a
17	NFIC	chr2:113304741-113305371	ECC-1	luminal epithelium:	n/a	n/a
18	CEBPB	chr2:113304933-113305254	IMR90	lung:	n/a	chr2:113305069-113305080
19	CEBPB	chr2:113304877-113305329	ECC-1	luminal epithelium:	n/a	chr2:113305069-113305080
20	STAT3	chr2:113304947-113305217	MCF10A-Er-Src	breast:	n/a	n/a
21	NFIC	chr2:113304829-113305369	ECC-1	luminal epithelium:	n/a	n/a
22	CEBPB	chr2:113304920-113305256	HepG2	liver:	n/a	chr2:113305069-113305080

No.	Distal block	Cell Line	Cell type
1	chr2:113300113..113302309-chr2:113304266..113305973,2	MCF-7	breast:
2	chr2:113305051..113306715-chr2:113310169..113312769,2	K562	blood:
3	chr2:113303031..113306151-chr2:113306991..113309484,3	K562	blood:
4	chr2:113252098..113253969-chr2:113305095..113307068,2	MCF-7	breast:
5	chr2:113235572..113240260-chr2:113300212..113305167,6	MCF-7	breast:

Variant related genes	Relation type
POLR1B	TF binding region
ENSG00000114999	Chromatin interaction
ENSG00000125630	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10153558	0.83[ASN][1000 genomes]
rs10153801	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10864905	0.91[ASN][1000 genomes]
rs11123140	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11123141	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11675730	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11676962	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677050	0.92[ASN][1000 genomes]
rs11689338	0.95[ASN][1000 genomes]
rs12618629	0.87[ASN][1000 genomes]
rs12618882	0.96[ASN][1000 genomes]
rs13015669	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1437673	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1437675	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1545133	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1595388	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304555	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35832933	0.86[ASN][1000 genomes]
rs3789723	0.96[ASN][1000 genomes]
rs3816140	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3816141	0.91[ASN][1000 genomes]
rs3961775	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3980067	0.82[ASN][1000 genomes]
rs41278940	0.99[ASN][1000 genomes]
rs41280572	0.91[ASN][1000 genomes]
rs4849072	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849073	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849074	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849075	0.96[ASN][1000 genomes]
rs4849076	0.99[ASN][1000 genomes]
rs56081241	0.91[ASN][1000 genomes]
rs60703755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7568539	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7578724	0.90[ASN][1000 genomes]
rs7607358	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11123139	TTL	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113301200-113307200	Weak transcription	HSMMtube	muscle
2	chr2:113301200-113340200	Weak transcription	Right Atrium	heart
3	chr2:113301200-113341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:113301400-113308800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:113301400-113308800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:113301400-113310000	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:113301400-113326200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:113301600-113305200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:113301600-113305200	Weak transcription	NHDF-Ad	bronchial
10	chr2:113301600-113305200	Weak transcription	NHLF	lung
11	chr2:113301600-113307600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:113301600-113308800	Weak transcription	Small Intestine	intestine
13	chr2:113301600-113316800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:113301600-113316800	Weak transcription	Stomach Mucosa	stomach
15	chr2:113301600-113325400	Weak transcription	Fetal Brain Male	brain
16	chr2:113301600-113325400	Weak transcription	Fetal Heart	heart
17	chr2:113303000-113320200	Strong transcription	K562	blood
18	chr2:113303000-113325400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:113303000-113325600	Strong transcription	Primary T cells from cord blood	blood
20	chr2:113303000-113334400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:113303000-113334400	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr2:113303000-113335200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:113303200-113313200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:113303200-113320200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:113303200-113334200	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:113303200-113334600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:113303400-113306400	Strong transcription	HepG2	liver
28	chr2:113303400-113308200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:113303400-113320200	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr2:113303400-113320200	Strong transcription	Fetal Intestine Large	intestine
31	chr2:113303400-113326200	Strong transcription	Primary B cells from cord blood	blood
32	chr2:113303400-113334400	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:113303400-113334600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:113303600-113306000	Strong transcription	Esophagus	oesophagus
35	chr2:113303600-113306400	Strong transcription	Primary hematopoietic stem cells	blood
36	chr2:113303600-113306400	Strong transcription	Brain Germinal Matrix	brain
37	chr2:113303600-113306600	Genic enhancers	Liver	Liver
38	chr2:113303600-113311600	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:113303600-113313400	Strong transcription	Brain Hippocampus Middle	brain
40	chr2:113303600-113314200	Strong transcription	NHEK	skin
41	chr2:113303600-113317000	Strong transcription	HUVEC	blood vessel
42	chr2:113303600-113317400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:113303600-113319800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr2:113303600-113320200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:113303600-113320400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr2:113303600-113320400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:113303600-113324400	Strong transcription	Fetal Brain Female	brain
48	chr2:113303600-113325400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr2:113303600-113325400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:113303600-113325800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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