Variant report

Variant	rs12741425
Chromosome Location	chr1:179366950-179366951
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179366133..179368260-chr1:179371106..179373571,2	K562	blood:

Extended variants
information (count: 114 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10913739	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs10913752	1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs10913753	1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs10913755	0.86[ASN][1000 genomes]
rs10913760	0.86[ASN][1000 genomes]
rs10913761	0.86[ASN][1000 genomes]
rs10913762	0.86[ASN][1000 genomes]
rs10913766	1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs10913767	1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs10913768	0.86[ASN][1000 genomes]
rs10913769	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10913770	0.86[ASN][1000 genomes]
rs10913771	0.86[ASN][1000 genomes]
rs11577579	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs11578241	0.86[ASN][1000 genomes]
rs11581659	0.87[EUR][1000 genomes]
rs11582158	0.84[CEU][hapmap];0.88[JPT][hapmap]
rs11582255	0.86[ASN][1000 genomes]
rs11582293	0.86[ASN][1000 genomes]
rs11582754	0.86[ASN][1000 genomes]
rs11586744	0.93[ASN][1000 genomes]
rs11801919	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11802624	0.86[ASN][1000 genomes]
rs11802625	0.86[ASN][1000 genomes]
rs11802637	0.86[ASN][1000 genomes]
rs11803938	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs11807559	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11811198	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12401957	1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs12403885	0.87[CHD][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap]
rs12403933	0.84[CEU][hapmap];0.84[GIH][hapmap];0.94[TSI][hapmap]
rs12408443	0.93[ASN][1000 genomes]
rs12409337	0.93[ASN][1000 genomes]
rs12722736	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12724320	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12724496	0.86[ASN][1000 genomes]
rs12724525	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12724634	0.86[ASN][1000 genomes]
rs12724778	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs12724901	0.84[CEU][hapmap];0.88[JPT][hapmap]
rs12725414	1.00[ASN][1000 genomes]
rs12726506	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs12726875	1.00[ASN][1000 genomes]
rs12729067	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12729775	0.86[ASN][1000 genomes]
rs12729788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12730056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12738262	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs12738929	0.86[ASN][1000 genomes]
rs12739116	0.86[ASN][1000 genomes]
rs12743018	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs12743585	0.93[ASN][1000 genomes]
rs12744251	0.86[ASN][1000 genomes]
rs12744438	1.00[ASN][1000 genomes]
rs12744949	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12744976	1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs12746253	1.00[ASN][1000 genomes]
rs12746331	0.92[EUR][1000 genomes]
rs12746578	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12747626	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12749461	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12750591	0.86[ASN][1000 genomes]
rs12751260	1.00[ASN][1000 genomes]
rs12751550	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12753162	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12753310	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12755634	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12755804	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12756624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12757708	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12757910	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12757935	0.93[ASN][1000 genomes]
rs12758415	0.93[ASN][1000 genomes]
rs12758828	0.84[CEU][hapmap];0.88[JPT][hapmap]
rs12760048	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12760534	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1410589	0.86[JPT][hapmap]
rs34315375	0.94[EUR][1000 genomes]
rs35978436	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3765548	0.85[CHD][hapmap]
rs3935240	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs4130266	1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs4233177	1.00[ASN][1000 genomes]
rs4233178	1.00[ASN][1000 genomes]
rs4233179	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4261076	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4360491	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4418554	0.93[ASN][1000 genomes]
rs4454499	0.86[ASN][1000 genomes]
rs4651028	1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs4652368	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4652383	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs61821011	0.86[ASN][1000 genomes]
rs6425536	0.88[GIH][hapmap];0.87[EUR][1000 genomes]
rs6666939	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7513782	0.93[ASN][1000 genomes]
rs7513973	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs7521106	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7524128	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs7532155	0.86[ASN][1000 genomes]
rs7550638	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs7551894	0.93[ASN][1000 genomes]
rs7554103	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7555722	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[YRI][hapmap]
rs7555895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9662026	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2762031	chr1:179323738-179375197	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
3	nsv518403	chr1:179323919-179371973	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv548279	chr1:179323919-179390148	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3514400	chr1:179349344-179400533	Enhancers Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3514401	chr1:179349344-179400533	Weak transcription Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3451112	chr1:179352344-179400533	Enhancers ZNF genes & repeats Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv523087	chr1:179352736-179371973	ZNF genes & repeats Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12741425	NPHS2	cis	cerebellum	SCAN
rs12741425	AXDND1	cis	Thyroid	GTEx
rs12741425	FIGF	trans	cerebellum	SCAN
rs12741425	TOR1AIP1	cis	cerebellum	SCAN
rs12741425	ZBTB37	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179366600-179367000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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