Variant report

Variant	rs541768
Chromosome Location	chr7:103375920-103375921
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	chr7:103374430..103376979-chr7:103378353..103381015,4	K562	blood:
2	chr7:103373703..103377683-chr7:103378422..103380704,3	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12540537	0.82[JPT][hapmap]
rs12705155	1.00[MEX][hapmap]
rs13239238	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1705109	1.00[MEX][hapmap]
rs2237633	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2299374	0.82[JPT][hapmap]
rs2299378	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2299379	0.83[JPT][hapmap]
rs2299380	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35441390	0.91[ASN][1000 genomes]
rs36011270	0.88[ASN][1000 genomes]
rs473940	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs477444	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs478549	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs491263	0.83[EUR][1000 genomes]
rs492063	1.00[MEX][hapmap]
rs495374	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs497536	0.82[LWK][hapmap];0.82[YRI][hapmap]
rs505394	0.81[EUR][1000 genomes]
rs507226	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs512529	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs525692	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs528528	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs531330	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs538258	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs554350	0.82[EUR][1000 genomes]
rs562393	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs562444	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs570418	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs571990	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs607755	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs618925	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs620243	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs620774	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621223	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs621311	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs622657	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62480693	0.87[ASN][1000 genomes]
rs62480700	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs635245	0.82[EUR][1000 genomes]
rs637577	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs637606	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs651097	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs671372	0.85[CEU][hapmap];0.89[ASN][1000 genomes]
rs682507	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs683390	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6953960	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7780986	0.90[EUR][1000 genomes];0.88[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	nsv491911	chr7:102967150-103403622	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv427799	chr7:103250733-103454202	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv518040	chr7:103375437-103379897	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv524344	chr7:103375437-103379897	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs541768	ATXN7L1	cis	parietal	SCAN
rs541768	ZAN	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:103374600-103376600	Enhancers	HUVEC	blood vessel
2	chr7:103375000-103376600	Enhancers	Muscle Satellite Cultured Cells	--
3	chr7:103375000-103376800	Enhancers	Hela-S3	cervix
4	chr7:103375200-103391000	Weak transcription	HepG2	liver
5	chr7:103375600-103376400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr7:103375600-103376400	Enhancers	NH-A	brain
7	chr7:103375600-103376600	Enhancers	HMEC	breast
8	chr7:103375600-103377000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:103375800-103376200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr7:103375800-103376600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:103375800-103376600	Enhancers	NHEK	skin

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