Variant report

Variant	rs11929069
Chromosome Location	chr3:142420213-142420214
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142418554..142422462-chr3:142423148..142426338,3	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10935467	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11915810	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11929107	0.83[CEU][hapmap]
rs13060062	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13064897	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13081200	0.92[GIH][hapmap];0.89[TSI][hapmap]
rs13081255	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs13087943	0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13092601	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13094259	0.92[GIH][hapmap];0.89[TSI][hapmap]
rs1916638	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34084493	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs34485065	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34941168	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36085850	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs55968753	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62278490	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62278492	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62278493	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62278494	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv591920	chr3:142411200-142496951	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv521098	chr3:142411200-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv520533	chr3:142417070-142440299	Weak transcription Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv518623	chr3:142417070-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11929069	SPSB4	cis	parietal	SCAN
rs11929069	TRPC1	cis	parietal	SCAN
rs11929069	ATP1B3	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142366000-142435400	Weak transcription	Colonic Mucosa	Colon
2	chr3:142389800-142442400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:142392800-142425400	Weak transcription	Dnd41	blood
4	chr3:142392800-142433000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:142393000-142426000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:142393400-142426200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:142408800-142430400	Weak transcription	Liver	Liver
8	chr3:142412800-142426600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:142413200-142422600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr3:142417800-142424200	Weak transcription	Rectal Mucosa Donor 31	rectum

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