Variant report

Variant	rs2124542
Chromosome Location	chr3:142712536-142712537
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:142547227..142548524-chr3:142712069..142713438,8	K562	blood:
2	chr3:142647753..142648651-chr3:142712531..142713417,3	MCF-7	breast:
3	chr3:142647572..142650450-chr3:142712421..142714563,2	K562	blood:
4	chr3:142647719..142648668-chr3:142712518..142713506,7	K562	blood:
5	chr3:142712027..142714851-chr3:142718551..142721851,5	MCF-7	breast:
6	chr3:142647689..142648573-chr3:142712288..142713030,2	MCF-7	breast:
7	chr3:142702341..142704530-chr3:142712048..142714578,2	MCF-7	breast:
8	chr3:142703024..142703532-chr3:142712151..142713027,2	K562	blood:
9	chr3:142297949..142299634-chr3:142710792..142712643,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000268129	Chromatin interaction
ENSG00000163714	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10413	0.92[EUR][1000 genomes]
rs1043898	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10451867	0.88[EUR][1000 genomes]
rs10513184	0.88[EUR][1000 genomes]
rs1053950	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10790	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10935474	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10935475	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935479	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11915462	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11922201	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12485790	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12490776	0.88[EUR][1000 genomes]
rs12492904	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695770	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13075955	0.88[EUR][1000 genomes]
rs13088422	0.81[EUR][1000 genomes]
rs13094293	0.91[EUR][1000 genomes]
rs13099995	0.81[EUR][1000 genomes]
rs1349262	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13715	0.89[EUR][1000 genomes]
rs1375814	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1449868	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1449869	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1530753	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1532588	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1545597	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17557029	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1814565	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1827159	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1839406	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1868569	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1868570	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1965343	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2045306	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2124541	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2124543	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2137586	0.93[EUR][1000 genomes]
rs2175739	0.93[EUR][1000 genomes]
rs2290549	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2353408	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2353409	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2353411	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3821645	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3856697	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3902877	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4030582	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4683444	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4683721	0.92[EUR][1000 genomes]
rs4683722	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4683723	0.87[EUR][1000 genomes]
rs4683724	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56382522	0.92[EUR][1000 genomes]
rs6440129	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6440131	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6440132	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6440133	0.82[EUR][1000 genomes]
rs6440134	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6770102	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778454	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6781080	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6781887	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6783145	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6796771	0.81[EUR][1000 genomes]
rs6802376	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6805417	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6806551	0.91[EUR][1000 genomes]
rs6808689	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7611721	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7623532	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7644475	0.88[EUR][1000 genomes]
rs7648143	0.91[EUR][1000 genomes]
rs7649225	0.86[EUR][1000 genomes]
rs7652745	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs766360	0.96[EUR][1000 genomes]
rs936194	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs936196	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs936197	0.88[EUR][1000 genomes]
rs937498	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9814656	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9816317	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9835348	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9847059	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9851353	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9862433	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9877128	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9877135	0.92[EUR][1000 genomes];0.84[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	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	nsv877563	chr3:142661350-142743889	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2124542	SR140	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142707000-142712600	Weak transcription	A549	lung
2	chr3:142707000-142715200	Weak transcription	Hela-S3	cervix
3	chr3:142707000-142716200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:142707000-142718800	Weak transcription	Right Ventricle	heart
5	chr3:142710200-142718600	Weak transcription	GM12878-XiMat	blood
6	chr3:142711000-142718400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:142712000-142712600	Weak transcription	Adipose Nuclei	Adipose
8	chr3:142712000-142713000	Enhancers	Liver	Liver
9	chr3:142712000-142713800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr3:142712000-142713800	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr3:142712200-142713000	Enhancers	K562	blood
12	chr3:142712200-142713200	Enhancers	HepG2	liver
13	chr3:142712200-142713600	Enhancers	Primary neutrophils fromperipheralblood	blood

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