Variant report

Variant	rs12490776
Chromosome Location	chr3:142786682-142786683
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142786465..142789211-chr3:142837997..142840855,2	K562	blood:
2	chr3:142720400..142721935-chr3:142786483..142788074,2	MCF-7	breast:
3	chr3:142781075..142783865-chr3:142785035..142788553,3	K562	blood:
4	chr3:142781075..142783865-chr3:142785035..142787679,2	K562	blood:
5	chr3:142771385..142780409-chr3:142780501..142789449,10	K562	blood:

Variant related genes	Relation type
ENSG00000175040	Chromatin interaction
ENSG00000163714	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10413	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1043898	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10451867	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513184	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1053950	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10790	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10935475	0.88[EUR][1000 genomes]
rs10935479	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11709036	0.84[EUR][1000 genomes]
rs11915462	0.90[EUR][1000 genomes]
rs11922201	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12485790	0.82[EUR][1000 genomes]
rs12492904	0.88[EUR][1000 genomes]
rs12695770	0.83[EUR][1000 genomes]
rs13075955	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13088422	0.83[EUR][1000 genomes]
rs13094293	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13099995	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1349262	0.95[EUR][1000 genomes]
rs13715	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375814	0.91[EUR][1000 genomes]
rs1449868	0.92[EUR][1000 genomes]
rs1449869	0.95[EUR][1000 genomes]
rs1530753	0.95[EUR][1000 genomes]
rs1532588	0.90[EUR][1000 genomes]
rs1545597	0.83[EUR][1000 genomes]
rs17557029	0.89[EUR][1000 genomes]
rs1814565	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1827159	0.95[EUR][1000 genomes]
rs1839406	0.92[EUR][1000 genomes]
rs1868569	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1868570	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1965343	0.91[EUR][1000 genomes]
rs2045306	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2124541	0.91[EUR][1000 genomes]
rs2124542	0.88[EUR][1000 genomes]
rs2124543	0.88[EUR][1000 genomes]
rs2137586	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2175739	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2290549	0.85[EUR][1000 genomes]
rs2353408	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2353409	0.95[EUR][1000 genomes]
rs2353411	0.95[EUR][1000 genomes]
rs3821645	0.95[EUR][1000 genomes]
rs3856697	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3902877	0.89[EUR][1000 genomes]
rs4030582	0.91[EUR][1000 genomes]
rs4683444	0.94[EUR][1000 genomes]
rs4683721	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683722	0.92[EUR][1000 genomes]
rs4683723	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683724	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56382522	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440129	0.91[EUR][1000 genomes]
rs6440131	0.94[EUR][1000 genomes]
rs6440132	0.92[EUR][1000 genomes]
rs6440133	0.87[EUR][1000 genomes]
rs6440134	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6770102	0.88[EUR][1000 genomes]
rs6778454	0.88[EUR][1000 genomes]
rs6781080	0.92[EUR][1000 genomes]
rs6781887	0.91[EUR][1000 genomes]
rs6783145	0.92[EUR][1000 genomes]
rs6784200	0.82[EUR][1000 genomes]
rs6796771	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6805417	0.95[EUR][1000 genomes]
rs6806551	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6808406	0.81[EUR][1000 genomes]
rs6808689	0.92[EUR][1000 genomes]
rs7611721	0.92[EUR][1000 genomes]
rs7623532	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7644475	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7648143	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7649225	0.92[EUR][1000 genomes]
rs7652745	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs766360	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs936194	0.95[EUR][1000 genomes]
rs936196	0.93[EUR][1000 genomes]
rs936197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937498	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9814656	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9816317	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9820175	0.81[EUR][1000 genomes]
rs9831162	0.82[EUR][1000 genomes]
rs9835348	0.92[EUR][1000 genomes]
rs9847059	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9851353	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9862433	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9875210	0.82[EUR][1000 genomes]
rs9877128	0.95[EUR][1000 genomes]
rs9877135	0.95[EUR][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	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS 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 target site	20 gene(s)	inside rSNPs	diseases
4	nsv591921	chr3:142762487-142841740	Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv1004467	chr3:142768867-142800605	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1004682	chr3:142768867-142804154	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12490776	SR140	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142763400-142787000	Weak transcription	Spleen	Spleen
2	chr3:142765400-142791600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:142769600-142789000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:142770400-142787000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:142771200-142790000	Weak transcription	Pancreas	Pancrea
6	chr3:142773000-142790200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:142773400-142788800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:142774200-142789400	Weak transcription	NHLF	lung
9	chr3:142775200-142789200	Weak transcription	NHDF-Ad	bronchial
10	chr3:142775400-142789200	Weak transcription	Primary T cells from cord blood	blood
11	chr3:142775400-142789400	Weak transcription	HSMMtube	muscle
12	chr3:142775600-142786800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:142775600-142794400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:142776000-142789600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:142776000-142789600	Weak transcription	NHEK	skin
16	chr3:142776200-142789400	Weak transcription	Osteobl	bone
17	chr3:142776200-142789600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:142776800-142789600	Weak transcription	NH-A	brain
19	chr3:142777000-142789400	Weak transcription	HMEC	breast
20	chr3:142778000-142786800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:142778000-142786800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:142778000-142789200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:142778000-142790400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:142778200-142786800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:142778200-142786800	Weak transcription	Fetal Thymus	thymus
26	chr3:142778200-142787800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:142778800-142790000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:142779000-142787000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:142780400-142789800	Weak transcription	K562	blood
30	chr3:142780800-142786800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:142780800-142789600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:142781000-142786800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:142781400-142786800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:142781400-142789400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:142782000-142789800	Weak transcription	Placenta	Placenta
36	chr3:142782200-142789400	Weak transcription	HSMM	muscle
37	chr3:142782800-142790000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:142784800-142786800	Enhancers	Fetal Stomach	stomach
39	chr3:142784800-142790000	Weak transcription	Fetal Intestine Small	intestine
40	chr3:142785600-142786800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:142786200-142789200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:142786400-142787400	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr3:142786400-142787400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:142786400-142789800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:142786400-142789800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:142786400-142789800	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:142786600-142786800	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr3:142786600-142787000	Enhancers	H9 Cell Line	embryonic stem cell
49	chr3:142786600-142787200	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr3:142786600-142788000	Enhancers	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links