Variant report

Variant	rs12699654
Chromosome Location	chr7:14730701-14730702
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	chr7:13321688..13322613-chr7:14730587..14732153,8	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10228891	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs10259838	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.93[ASN][1000 genomes]
rs10262035	0.85[EUR][1000 genomes]
rs10278975	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10499462	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11971649	0.82[CHB][hapmap];0.87[MEX][hapmap]
rs12533352	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12536592	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12537147	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12539208	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12669997	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12699655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12699658	0.83[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13231864	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13237347	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1357856	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs1357861	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs1357863	0.85[CEU][hapmap]
rs1357871	0.81[ASN][1000 genomes]
rs1357872	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1404613	0.89[CEU][hapmap];0.94[CHD][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1404614	0.89[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs1404615	0.85[CEU][hapmap]
rs1404616	0.85[CEU][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs1525074	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1525078	0.84[CEU][hapmap]
rs1525099	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs1568846	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1568847	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs17606181	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs17668635	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17668761	0.97[ASN][1000 genomes]
rs1997040	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2293339	0.89[CEU][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs34587189	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35046572	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35731392	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4521664	0.94[CHD][hapmap]
rs4719417	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4721360	0.81[ASN][1000 genomes]
rs6461120	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs6461121	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6944222	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6947566	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.95[ASN][1000 genomes]
rs6954517	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6956435	0.82[TSI][hapmap]
rs6956606	0.88[CEU][hapmap]
rs6965637	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6966274	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6974971	0.86[EUR][1000 genomes]
rs71538884	0.87[EUR][1000 genomes]
rs7784799	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs7785767	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7791900	0.88[CEU][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs885438	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9639210	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs9639212	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9639213	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9784967	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949033	chr7:14086106-14860323	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1031041	chr7:14624127-14999201	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv538741	chr7:14624127-14999201	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1015777	chr7:14661754-14730811	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv887712	chr7:14717872-14829858	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12699654	DGKB	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:14704200-14736000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr7:14712800-14775200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr7:14728800-14731400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr7:14730200-14730800	Enhancers	Primary hematopoietic stem cells	blood
5	chr7:14730200-14731400	Enhancers	Liver	Liver
6	chr7:14730400-14731400	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr7:14730400-14731400	Enhancers	Monocytes-CD14+_RO01746	blood

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