Variant report

Variant	rs1515950
Chromosome Location	chr2:87020817-87020818
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BRCA1	chr2:87020513-87021352	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
CD8A	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11547281	0.86[CHB][hapmap]
rs12612585	0.82[CHD][hapmap]
rs12994456	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13004867	1.00[JPT][hapmap]
rs13019439	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13023213	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13024420	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13024609	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13032379	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2944250	0.81[EUR][1000 genomes]
rs2944254	0.94[CEU][hapmap];0.86[TSI][hapmap]
rs3020726	1.00[ASN][1000 genomes]
rs3020728	0.87[ASN][1000 genomes]
rs34198915	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34256565	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34492196	1.00[ASN][1000 genomes]
rs34546581	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34613828	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34813683	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34855635	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34988194	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35290870	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35437846	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35505884	0.97[ASN][1000 genomes]
rs35626322	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35723887	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35739120	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35786939	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810831	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4366909	1.00[ASN][1000 genomes]
rs4605372	1.00[JPT][hapmap]
rs4832315	0.85[ASN][1000 genomes]
rs55816457	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55817008	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710361	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71411867	1.00[ASN][1000 genomes]
rs71411868	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71411869	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7596329	0.87[EUR][1000 genomes]

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	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv10063	chr2:86940988-87084360	Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1002420	chr2:86948835-87172715	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv874472	chr2:86961252-87071474	Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1008817	chr2:86970406-87172715	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv14382	chr2:86972214-87174121	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv997982	chr2:86972834-87105864	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1007746	chr2:86972834-87172715	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv458585	chr2:86974318-87108211	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv582373	chr2:86974318-87108211	Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv1007307	chr2:86974563-87055214	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv535809	chr2:86974563-87055214	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv1003748	chr2:86975514-87032318	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
14	nsv535810	chr2:86975514-87032318	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
15	nsv1004572	chr2:86975514-87082883	Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
16	nsv535811	chr2:86975514-87082883	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1515950	VPS24	cis	parietal	SCAN
rs1515950	POLR1A	cis	cerebellum	SCAN
rs1515950	RETSAT	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:87018800-87021000	Flanking Active TSS	Fetal Thymus	thymus
2	chr2:87018800-87022600	Weak transcription	Gastric	stomach
3	chr2:87019000-87021800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
4	chr2:87019600-87021400	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr2:87019600-87022000	Weak transcription	Spleen	Spleen
6	chr2:87020400-87021000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
7	chr2:87020400-87022400	Flanking Active TSS	Thymus	Thymus
8	chr2:87020600-87021800	Weak transcription	Dnd41	blood
9	chr2:87020800-87022800	Enhancers	Primary T cells from cord blood	blood
10	chr2:87020800-87023000	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr2:87020800-87023000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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