Variant report

Variant	rs2218240
Chromosome Location	chr4:143772767-143772768
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143767768..143770227-chr4:143771801..143773532,2	MCF-7	breast:
2	chr4:143766308..143769108-chr4:143769485..143773998,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USP38-1	chr4:143772645-143772804	XLOC_003714

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11100754	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs11100761	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11939835	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13112916	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13122287	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13145724	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372239	0.83[CHB][hapmap]
rs1373036	0.85[CHB][hapmap]
rs1441411	0.86[ASN][1000 genomes]
rs1441417	0.81[ASN][1000 genomes]
rs1441418	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1444950	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17016873	0.81[ASN][1000 genomes]
rs191762	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs1992652	0.83[ASN][1000 genomes]
rs28416530	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2874907	0.81[ASN][1000 genomes]
rs4575951	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4690698	0.92[CHB][hapmap]
rs4690699	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs4690728	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4690730	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60263370	0.83[ASN][1000 genomes]
rs6537124	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs6537127	0.88[ASN][1000 genomes]
rs6537130	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6811022	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6813785	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6824743	0.81[ASN][1000 genomes]
rs6831204	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6839158	0.88[CEU][hapmap];0.86[ASN][1000 genomes]
rs6846609	0.81[ASN][1000 genomes]
rs6852412	0.81[ASN][1000 genomes]
rs6852570	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs72615963	0.87[ASN][1000 genomes]
rs72728700	0.83[ASN][1000 genomes]
rs72730409	0.85[ASN][1000 genomes]
rs73850583	0.85[ASN][1000 genomes]
rs7660533	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7668263	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7670139	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7685997	0.83[ASN][1000 genomes]
rs877032	0.81[ASN][1000 genomes]
rs9994364	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880174	chr4:143639498-143848024	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 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	chr4:143768600-143781200	Weak transcription	Psoas Muscle	Psoas
2	chr4:143772200-143773800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:143772400-143772800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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