Variant report

Variant	rs9425862
Chromosome Location	chr1:180094699-180094700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr1:180067070..180070022-chr1:180093157..180094949,2	K562	blood:
4	chr1:180094467..180097034-chr1:180123312..180125749,2	K562	blood:
5	chr1:180094624..180096269-chr1:180125316..180126971,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260360	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000135837	Chromatin interaction
ENSG00000116260	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10798731	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798733	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913911	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10913912	1.00[ASN][1000 genomes]
rs10913913	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10913915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10913921	1.00[ASN][1000 genomes]
rs10913922	1.00[ASN][1000 genomes]
rs10913926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10913928	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913929	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589421	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12117957	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12119113	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120822	1.00[ASN][1000 genomes]
rs12124175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12124336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127248	1.00[ASN][1000 genomes]
rs12129928	1.00[ASN][1000 genomes]
rs12131995	1.00[ASN][1000 genomes]
rs12135952	1.00[ASN][1000 genomes]
rs12137562	1.00[CHB][hapmap]
rs12138251	1.00[ASN][1000 genomes]
rs12141545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12144757	1.00[ASN][1000 genomes]
rs12743903	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12744192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4083553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4652477	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4652478	1.00[ASN][1000 genomes]
rs55676403	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55882713	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56166206	1.00[ASN][1000 genomes]
rs58121876	1.00[ASN][1000 genomes]
rs59953116	1.00[ASN][1000 genomes]
rs61605706	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425605	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425608	0.87[EUR][1000 genomes]
rs6693288	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6702845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72710619	1.00[ASN][1000 genomes]
rs72710658	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521701	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7521873	1.00[ASN][1000 genomes]
rs7522347	1.00[CHB][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533903	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538086	1.00[ASN][1000 genomes]
rs7539784	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555418	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425484	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9425864	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[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

No data

Chromatin state (count:17 , 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	chr1:180089800-180095200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:180093000-180096200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:180093200-180095400	Weak transcription	NHEK	skin
13	chr1:180093200-180095600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:180093200-180095600	Weak transcription	K562	blood
15	chr1:180094000-180094800	Enhancers	Fetal Muscle Trunk	muscle
16	chr1:180094400-180095000	Enhancers	Placenta	Placenta
17	chr1:180094600-180098000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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