Variant report

Variant	rs6425609
Chromosome Location	chr1:180095348-180095349
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr1:180095261-180095454	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:179849546..179851570-chr1:180093822..180096311,2	K562	blood:
2	chr1:179922333..179925402-chr1:180094478..180098472,3	K562	blood:
3	chr1:180094856..180097003-chr1:180124933..180127557,2	K562	blood:
4	chr1:180094467..180097034-chr1:180123312..180125749,2	K562	blood:
5	chr1:180094976..180098396-chr1:180099565..180103492,4	MCF-7	breast:
6	chr1:180094624..180096269-chr1:180125316..180126971,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261817	TF binding region
ENSG00000116260	Chromatin interaction
ENSG00000135837	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000260360	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10753206	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10798729	0.88[CEU][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10798730	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798732	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10913917	0.96[CEU][hapmap]
rs10913927	0.81[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10913931	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12040314	0.92[CEU][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12040376	0.92[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12080763	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1297205	0.88[CEU][hapmap]
rs2477112	0.96[CEU][hapmap]
rs2477116	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2477118	0.81[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap]
rs2477120	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2501607	0.96[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2501610	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2501611	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2501613	0.81[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap]
rs2501615	0.95[CEU][hapmap]
rs2501617	0.88[CEU][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap]
rs2762859	0.96[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap]
rs3767200	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3767202	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3818999	0.80[ASW][hapmap];0.92[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3930305	0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4076449	0.96[CEU][hapmap];0.87[GIH][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4147169	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4256775	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4336810	0.92[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4506429	0.92[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4651057	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4652462	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4652463	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4652465	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4652470	0.81[GIH][hapmap]
rs4652471	0.92[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4652472	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4652473	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4652475	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs483307	0.96[CEU][hapmap]
rs500371	0.88[CEU][hapmap]
rs510209	0.96[CEU][hapmap]
rs528350	0.89[CEU][hapmap];0.80[CHD][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs534168	0.89[CEU][hapmap]
rs6425603	0.96[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6657347	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6691060	0.87[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6691435	0.92[CEU][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7524849	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7525385	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7551181	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9286932	0.96[CEU][hapmap];0.89[GIH][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9425481	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9425482	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9425483	0.88[ASW][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9425485	0.92[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9425486	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9425489	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9425849	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9425851	0.83[EUR][1000 genomes]
rs9425854	0.96[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9425855	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9425856	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9425860	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9425861	0.92[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9425863	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9425866	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9425868	0.92[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[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	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv1012558	chr1:180027960-180217613	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv535218	chr1:180027960-180217613	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv497930	chr1:180031321-180220723	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv533073	chr1:180031328-180217612	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv916937	chr1:180031328-180220685	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6425609	ASTN1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180084000-180096000	Weak transcription	Primary T cells from cord blood	blood
2	chr1:180086600-180100800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:180086600-180102400	Weak transcription	Pancreas	Pancrea
4	chr1:180087000-180097800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:180087200-180095600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:180087200-180095600	Weak transcription	Stomach Mucosa	stomach
7	chr1:180087200-180097000	Weak transcription	Lung	lung
8	chr1:180087200-180097400	Weak transcription	Esophagus	oesophagus
9	chr1:180089200-180097400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:180093000-180096200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:180093200-180095400	Weak transcription	NHEK	skin
12	chr1:180093200-180095600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:180093200-180095600	Weak transcription	K562	blood
14	chr1:180094600-180098000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:180095200-180096000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:180095200-180100200	Enhancers	Primary neutrophils fromperipheralblood	blood

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