Variant report

Variant	rs6778454
Chromosome Location	chr3:142711197-142711198
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142645933..142648284-chr3:142709421..142711755,2	K562	blood:
2	chr3:142699207..142701682-chr3:142709605..142712109,2	K562	blood:
3	chr3:142297949..142299634-chr3:142710792..142712643,2	MCF-7	breast:

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	0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10451867	0.88[EUR][1000 genomes]
rs10513184	0.88[EUR][1000 genomes]
rs1053950	0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10790	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10935474	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10935475	0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935479	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11915462	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11922201	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12485790	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12490776	0.88[EUR][1000 genomes]
rs12492904	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12695770	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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	0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13715	0.89[EUR][1000 genomes]
rs1375814	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1449868	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1449869	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1530753	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1532588	0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1545597	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17557029	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1814565	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1827159	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1839406	0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1868569	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1868570	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1965343	0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2045306	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2124541	0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2124542	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2124543	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2137586	0.93[EUR][1000 genomes]
rs2175739	0.93[EUR][1000 genomes]
rs2290549	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2353408	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2353409	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2353411	0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3821645	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3856697	0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3902877	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4030582	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4683444	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4683721	0.92[EUR][1000 genomes]
rs4683722	0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4683723	0.87[EUR][1000 genomes]
rs4683724	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56382522	0.92[EUR][1000 genomes]
rs6440129	0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6440131	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6440132	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6440133	0.82[EUR][1000 genomes]
rs6440134	0.84[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6770102	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6781080	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6781887	0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6783145	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6796771	0.81[EUR][1000 genomes]
rs6802376	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6805417	0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6806551	0.91[EUR][1000 genomes]
rs6808689	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7611721	0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7623532	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[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];0.80[ASN][1000 genomes]
rs766360	0.96[EUR][1000 genomes]
rs936194	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs936196	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs936197	0.88[EUR][1000 genomes]
rs937498	0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9814656	0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9816317	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9835348	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9847059	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9851353	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9862433	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9877128	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9877135	0.92[EUR][1000 genomes];0.83[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
rs6778454	SR140	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142707000-142712000	Weak transcription	Liver	Liver
2	chr3:142707000-142712200	Weak transcription	K562	blood
3	chr3:142707000-142712600	Weak transcription	A549	lung
4	chr3:142707000-142715200	Weak transcription	Hela-S3	cervix
5	chr3:142707000-142716200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:142707000-142718800	Weak transcription	Right Ventricle	heart
7	chr3:142710200-142718600	Weak transcription	GM12878-XiMat	blood
8	chr3:142710800-142711200	Flanking Active TSS	HepG2	liver
9	chr3:142711000-142718400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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