Variant report

Variant	rs529098
Chromosome Location	chr3:54677191-54677192
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10865990	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs11718583	0.88[ASW][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap]
rs17054369	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs1820616	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs1882321	0.90[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap]
rs1965072	0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs1965073	0.88[ASN][1000 genomes]
rs1997463	0.90[CHB][hapmap]
rs488451	0.86[ASN][1000 genomes]
rs492885	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4955890	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs510605	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs513324	0.88[GIH][hapmap]
rs525736	0.90[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs530868	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs533524	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs535526	0.94[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs541957	0.90[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs543828	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs550728	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs562668	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs566448	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs566884	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs568051	0.82[ASW][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.80[ASN][1000 genomes]
rs588784	0.94[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs596992	0.87[ASN][1000 genomes]
rs599573	0.94[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs601383	0.94[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs601420	0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.93[YRI][hapmap];0.88[ASN][1000 genomes]
rs608142	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs622326	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs623696	0.94[ASN][1000 genomes]
rs630987	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs634393	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs647480	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs652364	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs666071	0.94[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7633762	0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs838017	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9882650	0.90[CHB][hapmap];0.95[JPT][hapmap]

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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525644	chr3:54653316-54709987	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs529098	CXCL9	trans	brain	seeQTL
rs529098	GBP1	trans	brain	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54663600-54683800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:54674200-54677400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:54674400-54677800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr3:54674400-54678000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:54675000-54677200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:54675600-54677200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr3:54676000-54677200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr3:54676000-54677200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr3:54676200-54678000	Enhancers	H1 Cell Line	embryonic stem cell
10	chr3:54676400-54677800	Enhancers	H9 Cell Line	embryonic stem cell
11	chr3:54676400-54679000	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr3:54676600-54677200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:54676600-54677400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr3:54676800-54679200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr3:54676800-54683200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:54677000-54677200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr3:54677000-54677800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:54677000-54677800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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