Variant report

Variant	rs16862180
Chromosome Location	chr1:169413731-169413732
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169412248..169414010-chr1:169453413..169455967,2	MCF-7	breast:
2	chr1:169395119..169396871-chr1:169412478..169414358,2	K562	blood:

Variant related genes	Relation type
ENSG00000213062	Chromatin interaction
ENSG00000117477	Chromatin interaction
ENSG00000117479	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1028180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10753786	0.83[CHB][hapmap]
rs10800447	0.83[CHB][hapmap]
rs10919173	0.89[CHB][hapmap]
rs12040141	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12042044	0.82[EUR][1000 genomes]
rs12121994	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12143193	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12145146	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12145226	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12727318	0.80[AMR][1000 genomes]
rs12729761	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12733001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12733037	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12733626	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12744859	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12745541	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12751379	1.00[CEU][hapmap]
rs12752953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13306334	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1517745	0.89[CHB][hapmap]
rs1533518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1533519	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16862051	1.00[CEU][hapmap]
rs16862081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16862097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16862133	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16862153	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16862176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16862217	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1883167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2037249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2066001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2203743	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2271762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272801	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2300158	0.83[CHB][hapmap]
rs2301517	0.82[EUR][1000 genomes]
rs2420015	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2420016	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3213586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3213587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34057682	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34373126	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34599582	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34640648	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34858340	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34989506	0.80[AMR][1000 genomes]
rs35171152	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35686518	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35918529	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3765229	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3766083	1.00[CEU][hapmap]
rs3766084	1.00[CEU][hapmap]
rs3766090	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766097	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3862937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4140538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4140539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4551642	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4590731	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57295069	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58809384	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66512221	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6672589	0.89[CHB][hapmap]
rs66737090	0.86[EUR][1000 genomes]
rs66937324	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67795749	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724048	0.89[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs72637232	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7528751	1.00[CEU][hapmap]
rs7551623	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs929133	0.94[CHB][hapmap]
rs9332623	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9332624	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9332628	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9332647	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9332658	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9332678	1.00[CEU][hapmap]

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	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1001454	chr1:169387381-169465274	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1005941	chr1:169410486-169456393	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169413400-169418200	Weak transcription	Stomach Mucosa	stomach

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