Variant report

Variant	rs2121871
Chromosome Location	chr4:87800577-87800578
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87799265..87800918-chr4:87810195..87812041,2	K562	blood:
2	chr4:87514088..87517377-chr4:87799089..87802650,3	MCF-7	breast:
3	chr4:87799011..87801836-chr4:87812116..87814217,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163629	Chromatin interaction
ENSG00000163633	Chromatin interaction
ENSG00000109339	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10011798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10015121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10015477	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10015508	0.93[YRI][hapmap]
rs10021020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021790	0.90[ASN][1000 genomes]
rs10034336	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1010902	0.91[ASN][1000 genomes]
rs1010903	0.91[ASN][1000 genomes]
rs11097123	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11097124	0.81[ASN][1000 genomes]
rs11097125	0.98[EUR][1000 genomes]
rs12503045	0.98[EUR][1000 genomes]
rs12507165	0.98[EUR][1000 genomes]
rs12641570	0.98[EUR][1000 genomes]
rs13115795	0.90[ASN][1000 genomes]
rs13120981	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13137483	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1374935	1.00[EUR][1000 genomes]
rs17012132	0.92[ASN][1000 genomes]
rs17751557	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs1868244	0.96[CEU][hapmap];0.85[JPT][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs1985944	0.91[ASN][1000 genomes]
rs2594274	0.97[EUR][1000 genomes]
rs2594283	0.95[EUR][1000 genomes]
rs2705629	0.97[EUR][1000 genomes]
rs28446826	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28641910	0.94[ASN][1000 genomes]
rs28650493	0.94[ASN][1000 genomes]
rs28716151	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2904148	0.92[EUR][1000 genomes]
rs2904150	1.00[EUR][1000 genomes]
rs35428486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4235082	0.97[EUR][1000 genomes]
rs4693154	0.89[JPT][hapmap]
rs55698195	0.93[ASN][1000 genomes]
rs55889191	0.96[EUR][1000 genomes]
rs56062410	0.93[EUR][1000 genomes]
rs56201068	0.96[ASN][1000 genomes]
rs6531935	0.84[TSI][hapmap]
rs67758970	0.98[EUR][1000 genomes]
rs6823051	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6843070	0.96[CEU][hapmap];0.85[JPT][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs6846822	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72667703	0.91[ASN][1000 genomes]
rs72667705	0.90[ASN][1000 genomes]
rs727143	0.93[YRI][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	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2121871	PTPN13	cis	cerebellum	SCAN
rs2121871	AFF1	cis	cerebellum	SCAN
rs2121871	PTPN13	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87798800-87801200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:87800000-87800600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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