Variant report

Variant	rs12670599
Chromosome Location	chr7:11418931-11418932
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PHF14-1	chr7:11418914-11418996	ENSG00000230333.1
2	lnc-PHF14-1	chr7:11418914-11418993	ENSG00000230333.1
3	lnc-PHF14-1	chr7:11418914-11418996	ENSG00000230333.1
4	lnc-PHF14-1	chr7:11418324-11418996	ENSG00000230333.2
5	lnc-PHF14-1	chr7:11418914-11418996	ENSG00000230333.1

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10255748	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10950347	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs11766460	0.85[EUR][1000 genomes]
rs11772219	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11772248	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11772286	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1476566	1.00[CHB][hapmap]
rs17623777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1859225	0.91[CEU][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap]
rs1968059	0.89[CHB][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs1978137	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2018144	1.00[CHB][hapmap]
rs2023868	0.86[CHB][hapmap]
rs2023869	0.87[CHB][hapmap]
rs2107162	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189351	1.00[CEU][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs2189352	0.89[CHB][hapmap]
rs2285757	0.89[CHB][hapmap];0.86[YRI][hapmap]
rs38924	0.92[EUR][1000 genomes]
rs4351330	0.95[CEU][hapmap];0.96[GIH][hapmap];0.87[EUR][1000 genomes]
rs4636088	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4719273	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4720983	0.89[CHB][hapmap]
rs58102730	0.82[EUR][1000 genomes]
rs6460812	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6954956	0.85[ASN][1000 genomes]
rs6956916	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.90[ASN][1000 genomes]
rs6958033	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6962687	1.00[CEU][hapmap];0.96[GIH][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes]
rs6975177	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.87[ASN][1000 genomes]
rs6975407	0.83[ASW][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.87[MEX][hapmap]
rs757234	0.82[JPT][hapmap]
rs7777246	1.00[CEU][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs7777321	0.89[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7793926	0.83[EUR][1000 genomes]
rs7794215	0.82[JPT][hapmap]
rs7794515	0.89[EUR][1000 genomes]
rs7794645	0.88[ASN][1000 genomes]
rs7796389	0.89[CHB][hapmap]
rs7804531	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7810604	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7811128	0.89[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7811313	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.89[ASN][1000 genomes]
rs9986948	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019888	chr7:10712858-11496785	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1029836	chr7:10713523-11492751	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv538730	chr7:10713523-11492751	Weak transcription Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1024171	chr7:10810444-11559156	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv817291	chr7:10875417-11562683	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv523279	chr7:11198193-11473561	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv518180	chr7:11198193-11475819	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1015837	chr7:11208733-11475112	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv538732	chr7:11208733-11475112	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1028326	chr7:11221209-11754436	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv538733	chr7:11221209-11754436	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv830902	chr7:11336527-11523904	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1025802	chr7:11371145-11438472	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv830903	chr7:11384957-11586376	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv1032865	chr7:11395480-11477467	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12670599	NAALADL2	trans	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:11408000-11421000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:11408200-11430600	Weak transcription	Ovary	ovary
3	chr7:11413000-11430200	Weak transcription	Placenta	Placenta
4	chr7:11413200-11430200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr7:11413600-11430000	Weak transcription	Fetal Lung	lung
6	chr7:11414800-11419200	Weak transcription	Fetal Intestine Small	intestine
7	chr7:11415800-11419200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr7:11416800-11419000	Weak transcription	Liver	Liver
9	chr7:11417000-11440000	Weak transcription	Fetal Kidney	kidney
10	chr7:11418800-11419600	Strong transcription	Adipose Nuclei	Adipose

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