Variant report

Variant	rs401102
Chromosome Location	chr5:42873580-42873581
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	chr5:42849114..42851312-chr5:42872827..42874820,2	MCF-7	breast:

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10472376	1.00[ASN][1000 genomes]
rs13361827	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160332	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872962	1.00[ASN][1000 genomes]
rs16874465	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17300495	1.00[ASN][1000 genomes]
rs2444853	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548363	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548367	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548368	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2603635	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2924818	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309915	1.00[CHD][hapmap]
rs309920	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309933	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309937	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309943	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309944	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309945	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs315247	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs315248	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs315259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs315261	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs315265	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs315267	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs315268	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs315269	0.98[EUR][1000 genomes]
rs375476	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377822	0.88[CEU][hapmap];1.00[CHD][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs378886	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs387180	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs388377	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399923	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs401583	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404899	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs408180	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs410225	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs424862	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs426335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs427799	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs435255	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435445	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55736023	1.00[ASN][1000 genomes]
rs55962848	1.00[ASN][1000 genomes]
rs55981030	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56027646	1.00[ASN][1000 genomes]
rs56035132	1.00[ASN][1000 genomes]
rs56092116	1.00[ASN][1000 genomes]
rs56289342	1.00[ASN][1000 genomes]
rs56346893	1.00[ASN][1000 genomes]
rs57643758	1.00[ASN][1000 genomes]
rs57792463	1.00[ASN][1000 genomes]
rs60087060	1.00[ASN][1000 genomes]
rs60244620	1.00[ASN][1000 genomes]
rs6887414	1.00[ASN][1000 genomes]
rs72746737	1.00[ASN][1000 genomes]
rs72746739	1.00[ASN][1000 genomes]
rs72746746	1.00[ASN][1000 genomes]
rs72746753	1.00[ASN][1000 genomes]
rs72746762	1.00[ASN][1000 genomes]
rs72746766	1.00[ASN][1000 genomes]
rs72746768	1.00[ASN][1000 genomes]
rs72746770	1.00[ASN][1000 genomes]
rs72757078	1.00[ASN][1000 genomes]
rs72757080	1.00[ASN][1000 genomes]
rs72759052	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72759059	0.94[EUR][1000 genomes]
rs72759060	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72759061	0.94[EUR][1000 genomes]
rs72759062	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72759066	0.94[EUR][1000 genomes]
rs72759067	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72759071	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72759072	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72759073	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72759075	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72759077	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72759084	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72759085	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72759086	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72759087	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72759093	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72759095	1.00[ASN][1000 genomes]
rs72759097	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72762696	1.00[ASN][1000 genomes]
rs72762697	1.00[ASN][1000 genomes]
rs72762698	1.00[ASN][1000 genomes]
rs72762701	1.00[ASN][1000 genomes]
rs72764507	1.00[ASN][1000 genomes]
rs72764510	1.00[ASN][1000 genomes]
rs72764515	1.00[ASN][1000 genomes]
rs72764524	1.00[ASN][1000 genomes]
rs73754528	1.00[ASN][1000 genomes]
rs7702086	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
4	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
5	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
6	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv965602	chr5:42767568-42889585	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS 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	309 gene(s)	inside rSNPs	diseases
9	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
10	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
11	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42870200-42874000	Enhancers	HepG2	liver
2	chr5:42872200-42874600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr5:42872200-42875800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:42872200-42875800	Weak transcription	Placenta	Placenta
5	chr5:42872200-42876000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:42872400-42873800	Enhancers	Brain Substantia Nigra	brain
7	chr5:42872400-42875800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:42872600-42873600	Enhancers	Brain Anterior Caudate	brain
9	chr5:42872600-42873800	Flanking Active TSS	K562	blood
10	chr5:42872600-42882200	Enhancers	Fetal Intestine Large	intestine
11	chr5:42872600-42882400	Enhancers	Fetal Intestine Small	intestine
12	chr5:42873000-42874800	Enhancers	Liver	Liver
13	chr5:42873000-42876000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr5:42873200-42873800	Enhancers	Brain Hippocampus Middle	brain
15	chr5:42873400-42875800	Weak transcription	Colonic Mucosa	Colon
16	chr5:42873400-42875800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:42873400-42876000	Weak transcription	Brain Angular Gyrus	brain
18	chr5:42873400-42876600	Weak transcription	Brain Cingulate Gyrus	brain

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