Variant report

Variant	rs9995300
Chromosome Location	chr4:76993344-76993345
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76992822..76994466-chr4:76996001..76997996,2	K562	blood:
2	chr4:76988729..76991043-chr4:76993195..76994922,3	K562	blood:

Variant related genes	Relation type
ENSG00000156219	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10019066	0.88[AFR][1000 genomes]
rs10025961	0.87[AFR][1000 genomes]
rs10030471	0.88[AFR][1000 genomes]
rs10433952	0.85[AFR][1000 genomes]
rs12498973	0.88[YRI][hapmap]
rs12499668	0.91[LWK][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs12504339	0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs12509996	0.84[ASW][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap]
rs12510239	0.88[AFR][1000 genomes]
rs12511352	0.96[YRI][hapmap]
rs12511357	0.88[AFR][1000 genomes]
rs13106039	0.84[ASW][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs28484974	0.88[AFR][1000 genomes]
rs28601861	0.88[AFR][1000 genomes]
rs28647509	0.88[AFR][1000 genomes]
rs35028295	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs55813915	0.88[AFR][1000 genomes]
rs56054611	0.85[AFR][1000 genomes]
rs60282049	0.88[AFR][1000 genomes]
rs60431104	0.88[AFR][1000 genomes]
rs6532116	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6532167	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs6532168	0.84[ASW][hapmap];0.89[LWK][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs6532170	0.84[ASW][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs6532173	0.92[ASN][1000 genomes]
rs67194908	0.88[AFR][1000 genomes]
rs6834223	0.89[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72653702	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7666094	0.84[ASW][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs7685390	0.84[ASW][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs7693456	0.96[YRI][hapmap]
rs7693606	0.84[ASW][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap]
rs7698149	0.82[EUR][1000 genomes]
rs9307071	0.92[ASN][1000 genomes]
rs9990658	0.86[AFR][1000 genomes]
rs9998233	0.84[ASW][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv1009047	chr4:76989180-77077885	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9995300	CXCL11	cis	multi-tissue	Pritchard
rs9995300	ART3	cis	Nerve Tibial	GTEx
rs9995300	CDKL2	cis	cerebellum	SCAN
rs9995300	SHROOM3	cis	lymphoblastoid	seeQTL
rs9995300	SHROOM3	cis	cerebellum	SCAN
rs9995300	NUP54	cis	Nerve Tibial	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76992600-76993600	Enhancers	iPS-20b Cell Line	embryonic stem cell
2	chr4:76992600-76994800	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr4:76992800-76993600	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr4:76993200-76993600	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr4:76993200-76994800	Enhancers	HUES6 Cell Line	embryonic stem cell

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