Variant report

Variant	rs10187411
Chromosome Location	chr2:58237724-58237725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:58235603..58239393-chr2:58272093..58275370,6	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FANCL-1	chr2:58236367-58240741	ENSG00000250445
2	lnc-FANCL-1	chr2:58236367-58240741	NONHSAT070845

Variant related genes	Relation type
ENSG00000028116	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10164499	0.80[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.85[AMR][1000 genomes]
rs10165760	0.82[AFR][1000 genomes]
rs10174202	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10176681	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10178025	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10191766	0.87[AMR][1000 genomes]
rs10201793	0.87[AMR][1000 genomes]
rs10203014	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10518852	0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[AMR][1000 genomes]
rs11883874	0.87[LWK][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs11892302	0.84[AFR][1000 genomes]
rs11903212	0.80[MKK][hapmap];0.86[YRI][hapmap]
rs13382369	0.93[LWK][hapmap];1.00[MKK][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs13394820	0.84[AFR][1000 genomes]
rs13400997	0.87[AMR][1000 genomes]
rs13405281	0.82[AFR][1000 genomes]
rs13410500	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs13416900	0.95[YRI][hapmap]
rs13419989	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs13431271	0.90[LWK][hapmap];1.00[MKK][hapmap];0.87[AMR][1000 genomes]
rs1371213	0.95[YRI][hapmap]
rs1404460	0.86[YRI][hapmap]
rs2165100	0.91[LWK][hapmap];1.00[MKK][hapmap];0.82[AFR][1000 genomes]
rs2165103	0.85[YRI][hapmap]
rs2312486	1.00[YRI][hapmap]
rs28521626	0.84[AFR][1000 genomes]
rs4459722	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57112138	0.85[AFR][1000 genomes]
rs57597086	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58470176	0.82[AFR][1000 genomes]
rs6718190	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72949131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949137	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949158	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951048	0.82[AFR][1000 genomes]
rs72951056	0.82[AFR][1000 genomes]
rs7340170	0.90[YRI][hapmap]
rs7563225	0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.87[AMR][1000 genomes]
rs7563312	0.89[AFR][1000 genomes]
rs7569731	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7574578	0.84[YRI][hapmap];0.87[AMR][1000 genomes]
rs7574694	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7590976	0.85[MKK][hapmap];0.90[YRI][hapmap]
rs7600213	0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9309303	0.95[YRI][hapmap]
rs9973928	0.80[ASW][hapmap];0.84[LWK][hapmap];0.97[MKK][hapmap];0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834159	chr2:58101262-58283655	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv874200	chr2:58163178-58262016	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv458041	chr2:58196110-58237724	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv582096	chr2:58196110-58237724	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv999591	chr2:58214871-58316147	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58237200-58237800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:58237200-58238600	Enhancers	A549	lung
3	chr2:58237600-58237800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:58237600-58238000	Enhancers	HUVEC	blood vessel
5	chr2:58237600-58238200	Enhancers	HepG2	liver

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