Variant report

Variant	rs1991997
Chromosome Location	chr2:142646363-142646364
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:142645417..142646930-chr2:142887013..142889010,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168702	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10165154	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10181838	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs10182288	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10183142	0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10190657	0.99[ASN][1000 genomes]
rs10194554	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10198650	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10496906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap]
rs11693445	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs11884984	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11895935	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12467014	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap]
rs12471235	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs12611498	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12611558	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618005	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618032	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621414	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12623563	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12691627	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12995397	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13012265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap]
rs13013316	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs13024435	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13031056	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13408365	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13418027	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13429414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1369528	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1369530	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs1369542	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs1435598	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1435612	0.96[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1435616	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1529869	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap]
rs1561019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.81[TSI][hapmap]
rs16847640	0.82[CHB][hapmap]
rs1898018	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs1991998	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2196353	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2381169	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4662555	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4662557	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs6429927	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7558739	0.80[YRI][hapmap]
rs7569225	0.81[JPT][hapmap]
rs7579772	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7590166	0.81[ASN][1000 genomes]
rs7593594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7601913	0.83[YRI][hapmap]
rs7602677	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs9287326	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9789430	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530398	chr2:142474842-142843839	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1009893	chr2:142585905-142662116	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
3	nsv583238	chr2:142646363-142739121	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142640400-142647000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:142645000-142647200	Enhancers	Brain Inferior Temporal Lobe	brain
3	chr2:142646000-142647200	Enhancers	Brain Substantia Nigra	brain

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