Variant report

Variant	rs2881374
Chromosome Location	chr4:159039106-159039107
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:159036873..159039591-chr4:159040527..159042688,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10021199	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10517685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10517686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100152	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11933839	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11939690	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13130880	0.86[ASN][1000 genomes]
rs13137328	0.86[ASN][1000 genomes]
rs13137541	0.86[ASN][1000 genomes]
rs17036992	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036995	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17037201	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17037232	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17212066	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17212714	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17271385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17279270	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2594759	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2594760	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2725492	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs2725504	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2725505	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2725506	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2725507	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2725508	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs4234916	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs4443327	0.86[ASN][1000 genomes]
rs4508943	1.00[CHB][hapmap]
rs4510503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs4549446	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs4608853	0.86[ASN][1000 genomes]
rs6536289	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs6536290	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs6536294	0.86[ASN][1000 genomes]
rs6815974	0.86[ASN][1000 genomes]
rs6820988	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6834839	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6837943	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691603	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72691606	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72691610	0.81[EUR][1000 genomes]
rs72691615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691622	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691626	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691627	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691629	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691632	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691633	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691634	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691636	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691649	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72695726	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72695736	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72695741	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72695744	0.90[EUR][1000 genomes]
rs72695745	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72695747	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72695748	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72695749	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72695750	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72695751	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72695753	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7664129	0.86[ASN][1000 genomes]
rs7678302	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9997618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[ASN][1000 genomes]

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	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1021067	chr4:158972282-159175475	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv880293	chr4:159012365-159049020	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2881374	RP11-597D13.9	cis	Esophagus Muscularis	GTEx
rs2881374	FLJ11155	cis	multi-tissue	Pritchard
rs2881374	TMEM144	cis	Esophagus Muscularis	GTEx
rs2881374	DKFZp434L142	cis	multi-tissue	Pritchard

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159031400-159042000	Weak transcription	Fetal Heart	heart
2	chr4:159033600-159042400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr4:159034200-159046200	Weak transcription	HUVEC	blood vessel
4	chr4:159035000-159041200	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr4:159038800-159039600	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr4:159039000-159042600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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