Variant report

Variant	rs251486
Chromosome Location	chr3:142706340-142706341
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:142623173..142624153-chr3:142705646..142706555,2	K562	blood:
2	chr3:142547386..142547981-chr3:142705677..142706489,2	MCF-7	breast:
3	chr3:142547322..142548218-chr3:142705325..142706773,4	MCF-7	breast:
4	chr3:142647631..142648220-chr3:142705617..142706573,2	MCF-7	breast:
5	chr3:142648243..142649217-chr3:142705740..142706552,4	MCF-7	breast:
6	chr3:142706036..142707865-chr3:142708223..142711029,2	K562	blood:
7	chr3:142647658..142648658-chr3:142705658..142706609,3	K562	blood:
8	chr3:142705633..142707723-chr3:142715546..142717712,2	MCF-7	breast:

No data

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10790	0.85[CEU][hapmap]
rs185182	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2175739	0.82[CEU][hapmap]
rs2290549	0.85[CEU][hapmap]
rs251484	0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs251485	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs251487	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs251489	0.89[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs251490	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs251491	0.96[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs251492	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3101060	0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs36284	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36285	0.96[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs40160	0.85[JPT][hapmap];0.80[AMR][1000 genomes]
rs668856	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7652745	0.85[CEU][hapmap]

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
rs251486	SR140	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142700600-142706400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:142700600-142706600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:142701400-142706400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:142701400-142708200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:142701600-142706400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:142701600-142706400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:142701600-142706400	Weak transcription	A549	lung
8	chr3:142701600-142706600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:142701800-142706400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:142703200-142707000	Enhancers	K562	blood
11	chr3:142705800-142707000	Enhancers	Liver	Liver
12	chr3:142706000-142706400	Weak transcription	Left Ventricle	heart
13	chr3:142706000-142706600	Enhancers	Fetal Brain Male	brain
14	chr3:142706000-142706600	Weak transcription	Right Atrium	heart
15	chr3:142706000-142706800	Enhancers	HepG2	liver
16	chr3:142706000-142707000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:142706200-142706800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:142706200-142706800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr3:142706200-142706800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:142706200-142707000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:142706200-142707000	Enhancers	Fetal Stomach	stomach

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