Variant report

Variant	rs553369
Chromosome Location	chrX:154963439-154963440
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 63 )

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

rs_ID	r²[population]
rs10782079	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1084450	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs473491	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap]
rs473529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs473772	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs476928	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs479901	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap]
rs498000	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap]
rs561928	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs574386	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap]
rs580468	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap]
rs5940376	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap]
rs5940478	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs5940479	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap]
rs5940484	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap]
rs5940486	0.88[JPT][hapmap]
rs5940539	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap]
rs5983658	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap]
rs5983743	0.90[CHB][hapmap];0.95[CHD][hapmap]
rs628761	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs674707	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs89278	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532965	chrX:154418093-155226096	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv532967	chrX:154418093-155252027	Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv915940	chrX:154577793-155232907	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers 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 miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534441	chrX:154664337-155251871	Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv869305	chrX:154739403-155190347	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv916736	chrX:154762193-155232894	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv917356	chrX:154906586-154993039	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv471607	chrX:154906586-155041994	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
9	esv3441367	chrX:154906586-155188122	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
10	esv3411323	chrX:154906586-155189683	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv529629	chrX:154908412-155181583	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv534220	chrX:154929220-155251871	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
13	esv16887	chrX:154929773-154963593	Flanking Active TSS Enhancers Active TSS Weak transcription	n/a	n/a	inside rSNPs	n/a
14	nsv529342	chrX:154946830-155142026	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
15	nsv532993	chrX:154946830-155251871	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
16	esv3366519	chrX:154963291-155133665	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:63)

SNP	Gene	Cis/trans	Tissue	Source
rs553369	DDX3X	trans	lymphoblastoid	seeQTL
rs553369	CYorf15B	trans	multi-tissue	Pritchard
rs553369	RPS4Y2P	trans	multi-tissue	Pritchard
rs553369	CYorf15A	trans	multi-tissue	Pritchard
rs553369	TMLHE	trans	multi-tissue	Pritchard
rs553369	TTTY15	trans	multi-tissue	Pritchard
rs553369	EIF1AX	trans	multi-tissue	Pritchard
rs553369	EIF2S3	trans	lymphoblastoid	seeQTL
rs553369	USP9Y	trans	lymphoblastoid	seeQTL
rs553369	BOLA3	trans	multi-tissue	Pritchard
rs553369	U2AF1L2	trans	multi-tissue	Pritchard
rs553369	UTY	trans	lymphoblastoid	seeQTL
rs553369	KDM6A	trans	lymphoblastoid	seeQTL
rs553369	DDX3Y	trans	lymphoblastoid	seeQTL
rs553369	USP9Y	trans	multi-tissue	Pritchard
rs553369	EFHC2	trans	multi-tissue	Pritchard
rs553369	KAL1	trans	lymphoblastoid	seeQTL
rs553369	UBE1	trans	multi-tissue	Pritchard
rs553369	CYorf14	trans	multi-tissue	Pritchard
rs553369	CLC	trans	multi-tissue	Pritchard
rs553369	UTX	trans	multi-tissue	Pritchard
rs553369	ZFY	trans	multi-tissue	Pritchard
rs553369	ARSD	trans	multi-tissue	Pritchard
rs553369	MMP9	trans	multi-tissue	Pritchard
rs553369	GATA2	trans	multi-tissue	Pritchard
rs553369	RPS4Y1	trans	lymphoblastoid	seeQTL
rs553369	RPS4X	trans	lymphoblastoid	seeQTL
rs553369	MELL1	trans	multi-tissue	Pritchard
rs553369	XIST	trans	lymphoblastoid	seeQTL
rs553369	EIF1AY	trans	multi-tissue	Pritchard
rs553369	CYorf15B	trans	lymphoblastoid	seeQTL
rs553369	LOC646786	trans	multi-tissue	Pritchard
rs553369	TRPM4	trans	multi-tissue	Pritchard
rs553369	PRKY	trans	multi-tissue	Pritchard
rs553369	KDM5C	trans	lymphoblastoid	seeQTL
rs553369	EIF1AX	trans	lymphoblastoid	seeQTL
rs553369	PRKY	trans	lymphoblastoid	seeQTL
rs553369	KDM5D	trans	lymphoblastoid	seeQTL
rs553369	ZFX	trans	multi-tissue	Pritchard
rs553369	TTTY15	trans	lymphoblastoid	seeQTL
rs553369	PTK2	trans	multi-tissue	Pritchard
rs553369	CD99	trans	lymphoblastoid	seeQTL
rs553369	DDX3Y	trans	multi-tissue	Pritchard
rs553369	PNPLA4	trans	lymphoblastoid	seeQTL
rs553369	TMSB4Y	trans	multi-tissue	Pritchard
rs553369	PRKX	trans	multi-tissue	Pritchard
rs553369	FCGR2B	trans	multi-tissue	Pritchard
rs553369	NLGN4Y	trans	lymphoblastoid	seeQTL
rs553369	UTY	trans	multi-tissue	Pritchard
rs553369	SMCX	trans	multi-tissue	Pritchard
rs553369	CMKOR1	trans	multi-tissue	Pritchard
rs553369	HDHD1A	trans	multi-tissue	Pritchard
rs553369	SMC1A	trans	lymphoblastoid	seeQTL
rs553369	RPS4Y1	trans	multi-tissue	Pritchard
rs553369	EIF2S3	trans	multi-tissue	Pritchard
rs553369	SMCY	trans	multi-tissue	Pritchard
rs553369	PDGFRB	trans	multi-tissue	Pritchard
rs553369	EIF1AY	trans	lymphoblastoid	seeQTL
rs553369	HDHD1	trans	lymphoblastoid	seeQTL
rs553369	TMSB4Y	trans	lymphoblastoid	seeQTL
rs553369	ZRSR2	trans	lymphoblastoid	seeQTL
rs553369	LOC647322	trans	multi-tissue	Pritchard
rs553369	XIST	trans	multi-tissue	Pritchard

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:154963400-154963800	Enhancers	Stomach Mucosa	stomach
2	chrX:154963400-154964000	Weak transcription	Aorta	Aorta

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