Variant report

Variant	rs1328285
Chromosome Location	chr9:15922137-15922138
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNAPC3-1	chr9:15922109-15922200	NONHSAT130279

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1080484	0.87[ASW][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.85[YRI][hapmap]
rs1169469	0.88[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1169471	1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1169472	1.00[JPT][hapmap];0.85[TSI][hapmap];0.92[ASN][1000 genomes]
rs1169475	0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1169476	0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1169477	0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs1169481	1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1169482	0.85[ASN][1000 genomes]
rs1184568	0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.92[ASN][1000 genomes]
rs1184913	0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1186048	0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1186387	0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs1328287	0.81[TSI][hapmap];0.91[EUR][1000 genomes]
rs1341733	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1359952	0.85[YRI][hapmap]
rs1536686	0.93[EUR][1000 genomes]
rs1536687	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs16933738	0.92[ASN][1000 genomes]
rs1773062	0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1891209	0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.92[ASN][1000 genomes]
rs1935223	0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs2094519	0.81[TSI][hapmap]
rs2094520	0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2182934	1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2182935	1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2769714	0.92[ASN][1000 genomes]
rs2769716	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794638	0.85[ASN][1000 genomes]
rs2987009	0.81[YRI][hapmap]
rs2987012	0.81[YRI][hapmap]
rs2987037	0.93[ASN][1000 genomes]
rs2987040	0.93[ASN][1000 genomes]
rs2987043	0.93[ASN][1000 genomes]
rs2987044	0.93[ASN][1000 genomes]
rs2987046	0.85[ASN][1000 genomes]
rs2987053	0.92[ASN][1000 genomes]
rs2987054	1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2987057	1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2987063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987064	0.95[EUR][1000 genomes]
rs2987065	1.00[ASW][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987066	0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2987073	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2987076	1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2987077	0.85[ASN][1000 genomes]
rs3008666	0.80[YRI][hapmap]
rs3008669	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3008680	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3008681	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs3008682	1.00[ASW][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3008683	1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3008684	0.85[EUR][1000 genomes]
rs3008700	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3008706	0.85[ASN][1000 genomes]
rs3008708	0.85[ASN][1000 genomes]
rs3008712	0.93[ASN][1000 genomes]
rs3008737	0.93[ASN][1000 genomes]
rs3008748	0.81[YRI][hapmap]
rs3750402	1.00[ASN][1000 genomes]
rs6474996	0.93[ASN][1000 genomes]
rs7469281	1.00[ASN][1000 genomes]
rs770193	0.85[TSI][hapmap]
rs770194	0.81[TSI][hapmap]
rs770197	0.80[EUR][1000 genomes]
rs770203	1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs770204	0.81[TSI][hapmap]
rs770205	0.81[TSI][hapmap]
rs770206	1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs770209	1.00[JPT][hapmap]
rs770210	0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.92[ASN][1000 genomes]
rs770212	0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.92[ASN][1000 genomes]
rs770214	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs770216	1.00[JPT][hapmap]
rs770217	1.00[ASN][1000 genomes]
rs770218	0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.92[ASN][1000 genomes]
rs7860856	0.81[ASN][1000 genomes]
rs961116	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2753625	chr9:15914055-15980320	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	lncRNA	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15918200-15930800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr9:15920000-15936000	Weak transcription	Ovary	ovary
3	chr9:15920600-15922800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:15920800-15922800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:15921600-15924800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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