Variant report

Variant	rs3766052
Chromosome Location	chr1:169126031-169126032
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	chr1:169124501..169127273-chr1:169133900..169136216,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10800430	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10919073	1.00[CEU][hapmap]
rs10919079	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919097	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919098	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919100	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919104	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919109	0.84[EUR][1000 genomes]
rs10919110	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10919111	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919131	0.87[AMR][1000 genomes]
rs10919151	0.82[EUR][1000 genomes]
rs1138486	1.00[CEU][hapmap]
rs11802239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805562	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11806445	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11807896	0.82[EUR][1000 genomes]
rs11810815	0.82[EUR][1000 genomes]
rs1200152	0.88[ASN][1000 genomes]
rs12058325	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12060959	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12061080	0.82[EUR][1000 genomes]
rs12061405	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12062884	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12063719	0.87[AMR][1000 genomes]
rs12065030	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs12067351	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12070031	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12071122	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12071224	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12073439	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12074013	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12074492	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12076519	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12079745	1.00[CEU][hapmap]
rs12081562	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12082748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12083249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12088672	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12089602	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12097260	0.82[EUR][1000 genomes]
rs12097682	0.82[EUR][1000 genomes]
rs12561922	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap]
rs12740226	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2275300	0.82[EUR][1000 genomes]
rs2982468	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35144581	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3753298	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3766040	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3766064	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766082	1.00[CEU][hapmap];0.81[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3766088	1.00[CEU][hapmap];0.81[GIH][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs3766092	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3820057	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61806984	0.81[AMR][1000 genomes]
rs9628661	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	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

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169091800-169137600	Weak transcription	Esophagus	oesophagus
2	chr1:169096600-169137400	Weak transcription	Fetal Stomach	stomach
3	chr1:169097000-169130000	Weak transcription	Ovary	ovary
4	chr1:169100800-169141400	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:169101000-169137000	Weak transcription	Primary T cells from cord blood	blood
6	chr1:169103400-169130200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:169104800-169142800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:169115800-169130400	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:169116200-169130200	Weak transcription	Brain Anterior Caudate	brain
10	chr1:169116400-169126600	Weak transcription	Right Atrium	heart
11	chr1:169116400-169139400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:169118000-169137000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:169118200-169130400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:169118400-169126400	Weak transcription	Small Intestine	intestine
15	chr1:169118600-169130000	Weak transcription	Liver	Liver
16	chr1:169120400-169130200	Weak transcription	A549	lung
17	chr1:169121000-169129200	Weak transcription	Lung	lung
18	chr1:169121000-169137000	Weak transcription	Psoas Muscle	Psoas
19	chr1:169121000-169140800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:169121200-169141200	Weak transcription	Left Ventricle	heart
21	chr1:169121800-169143000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:169122600-169130200	Weak transcription	NHEK	skin
23	chr1:169122800-169136400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:169124200-169127600	Enhancers	Fetal Intestine Large	intestine
25	chr1:169124400-169128000	Enhancers	Fetal Intestine Small	intestine
26	chr1:169124600-169130200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:169124800-169130800	Weak transcription	Gastric	stomach
28	chr1:169124800-169138800	Weak transcription	Primary B cells from cord blood	blood
29	chr1:169125000-169126200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:169125200-169126800	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr1:169125400-169126200	Weak transcription	Fetal Heart	heart
32	chr1:169125400-169130000	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:169125400-169130200	Weak transcription	Right Ventricle	heart
34	chr1:169125400-169131200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:169125600-169126600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:169125800-169126400	Weak transcription	Colonic Mucosa	Colon
37	chr1:169126000-169127000	Enhancers	Stomach Mucosa	stomach

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