Variant report

Variant	rs5998478
Chromosome Location	chr22:32811952-32811953
allele	A/G
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	22:32292186-32294405..22:32809335-32812035	Hela-S3	cervix:
2	22:32477762-32487457..22:32809335-32812035	Hela-S3	cervix:
3	22:32012966-32043914..22:32809335-32812035	Hela-S3	cervix:
4	chr22:32807783..32810463-chr22:32811648..32815260,3	MCF-7	breast:
5	22:32809335-32812035..22:32872511-32874561	Hela-S3	cervix:
6	22:32188129-32210582..22:32809335-32812035	Hela-S3	cervix:
7	22:32809335-32812035..22:32860159-32865649	H1-hESC	embryonic stem cell:	embryo
8	22:32334260-32338420..22:32809335-32812035	K562	blood:
9	22:32809335-32812035..22:32868055-32872511	Hela-S3	cervix:
10	22:32053085-32061138..22:32809335-32812035	Hela-S3	cervix:
11	22:32809335-32812035..22:33452523-33459358	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000185666	Chromatin interaction
ENSG00000100170	Chromatin interaction
ENSG00000100220	Chromatin interaction
ENSG00000128254	Chromatin interaction
ENSG00000184459	Chromatin interaction
ENSG00000100225	Chromatin interaction
ENSG00000241878	Chromatin interaction
ENSG00000100150	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12168441	0.82[YRI][hapmap]
rs1543320	0.82[CHB][hapmap]
rs16990428	0.83[CHB][hapmap]
rs16990430	0.83[CHB][hapmap]
rs2049946	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049947	0.89[ASN][1000 genomes]
rs2072815	0.87[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2072817	0.82[YRI][hapmap]
rs2072818	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2076036	0.82[YRI][hapmap]
rs2076045	0.83[CHB][hapmap]
rs2076048	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs2076049	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2142720	0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs2281035	0.83[CHB][hapmap]
rs2281036	0.86[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs2294312	0.86[ASN][1000 genomes]
rs2294313	0.82[CHB][hapmap]
rs2413113	0.87[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs4140572	0.83[CHB][hapmap]
rs5749421	0.89[ASN][1000 genomes]
rs5749426	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs5749428	0.83[CHB][hapmap]
rs5749429	0.83[CHB][hapmap]
rs5749432	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs5754063	0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs5754065	0.83[CHB][hapmap]
rs5754066	0.91[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs5754081	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs5994562	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5998471	0.87[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs5998475	0.83[CHB][hapmap]
rs60953467	0.84[ASN][1000 genomes]
rs713790	0.83[CHB][hapmap]
rs7287452	0.91[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.84[ASN][1000 genomes]
rs737779	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs742096	0.83[CHB][hapmap]
rs9619262	0.91[YRI][hapmap]

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	nsv459874	chr22:32574274-32866934	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv588895	chr22:32574274-32866934	Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1064737	chr22:32603912-32829725	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1066118	chr22:32779078-32815334	Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1055701	chr22:32806595-32845403	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs5998478	RAB27A	trans	cerebellum	SCAN
rs5998478	OSBP2	cis	cerebellum	SCAN
rs5998478	CCDC157	cis	parietal	SCAN
rs5998478	AMICA1	trans	lymphoblastoid	seeQTL
rs5998478	C22orf28	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32808200-32818000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr22:32808400-32818000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr22:32809000-32814000	Weak transcription	GM12878-XiMat	blood
4	chr22:32809000-32817600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr22:32810200-32817000	Weak transcription	Liver	Liver

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