Variant report

Variant	rs990739
Chromosome Location	chr3:142926765-142926766
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142921678..142924452-chr3:142925121..142926893,2	K562	blood:
2	chr3:142926220..142927861-chr3:142959735..142962076,2	K562	blood:
3	chr3:142910443..142912503-chr3:142926393..142928620,2	K562	blood:
4	chr3:142925537..142928123-chr3:142932131..142934327,2	K562	blood:
5	chr3:142917669..142921522-chr3:142924910..142927664,3	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10470450	0.81[EUR][1000 genomes]
rs13317029	0.80[EUR][1000 genomes]
rs1372288	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1604377	1.00[JPT][hapmap]
rs17470684	0.87[ASN][1000 genomes]
rs4553947	0.97[EUR][1000 genomes]
rs4839604	0.80[EUR][1000 genomes]
rs60818974	0.97[EUR][1000 genomes]
rs6775385	0.95[EUR][1000 genomes]
rs6785254	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73006209	0.84[EUR][1000 genomes]
rs7627757	0.84[EUR][1000 genomes]
rs7631070	0.81[EUR][1000 genomes]
rs894180	0.97[EUR][1000 genomes]
rs920570	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821183	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829667	0.97[EUR][1000 genomes]
rs9842703	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs9849247	0.97[EUR][1000 genomes]
rs985247	0.82[EUR][1000 genomes]
rs9862637	0.95[EUR][1000 genomes]
rs9879103	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv508250	chr3:142842454-142943722	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv34280	chr3:142887460-142962075	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv818171	chr3:142894411-142960273	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1009573	chr3:142896048-142959777	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv2757014	chr3:142905661-142964373	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs990739	BIN1	cis	Brain Pons	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142924800-142927000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:142925000-142927600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:142925200-142926800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:142925200-142927000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:142925600-142926800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:142925600-142926800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:142925800-142926800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr3:142925800-142927000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr3:142925800-142927400	Enhancers	K562	blood
10	chr3:142925800-142932200	Enhancers	Fetal Thymus	thymus
11	chr3:142926000-142926800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:142926000-142926800	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr3:142926000-142927000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr3:142926000-142927000	Flanking Active TSS	GM12878-XiMat	blood
15	chr3:142926000-142929800	Enhancers	Thymus	Thymus
16	chr3:142926200-142926800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:142926200-142927200	Flanking Active TSS	Dnd41	blood
18	chr3:142926400-142928800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:142926400-142928800	Weak transcription	Brain Anterior Caudate	brain
20	chr3:142926600-142926800	Enhancers	Fetal Kidney	kidney
21	chr3:142926600-142928400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:142926600-142937200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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