Variant report

Variant	rs10800488
Chromosome Location	chr1:169886587-169886588
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	chr1:169885836..169887922-chr1:169893783..169895856,2	MCF-7	breast:
2	chr1:169881052..169883977-chr1:169885843..169888269,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10489175	1.00[CEU][hapmap]
rs11577641	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs11579102	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs11579254	1.00[CEU][hapmap]
rs11582552	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11584208	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11585093	0.84[EUR][1000 genomes]
rs11588736	1.00[CEU][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs11589659	1.00[CEU][hapmap]
rs11589671	1.00[CEU][hapmap]
rs11590604	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs1360294	0.88[CEU][hapmap];0.95[MEX][hapmap]
rs1572551	1.00[CEU][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16828209	1.00[CEU][hapmap]
rs16862683	1.00[CEU][hapmap]
rs16862870	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16862874	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16862902	1.00[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs1928887	1.00[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs2420510	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[MEX][hapmap]
rs2420511	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap]
rs35196850	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3753312	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs3766138	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[MEX][hapmap]
rs3766145	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[TSI][hapmap]
rs3766146	1.00[CEU][hapmap]
rs3766150	1.00[ASW][hapmap];0.88[CEU][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs3817859	1.00[CEU][hapmap];0.80[TSI][hapmap]
rs3917428	0.87[CEU][hapmap]
rs3917432	0.87[CEU][hapmap]
rs41496844	1.00[CEU][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4656198	0.89[ASW][hapmap]
rs4656201	0.85[EUR][1000 genomes]
rs4656202	1.00[CEU][hapmap]
rs4656718	0.89[ASW][hapmap]
rs4656726	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs4656727	0.82[EUR][1000 genomes]
rs4656732	1.00[CEU][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs55806711	0.85[EUR][1000 genomes]
rs61806076	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61806098	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61807835	0.83[EUR][1000 genomes]
rs61807840	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61825319	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6685211	1.00[CEU][hapmap]
rs73026253	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73035088	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169872800-169887800	Weak transcription	Primary T cells from cord blood	blood
2	chr1:169875800-169889800	Weak transcription	Fetal Brain Female	brain
3	chr1:169876200-169903600	Weak transcription	Aorta	Aorta
4	chr1:169877600-169889800	Weak transcription	Lung	lung
5	chr1:169878400-169892200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr1:169878400-169895200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:169878400-169946200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:169878600-169895000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:169880200-169892800	Weak transcription	Fetal Heart	heart
10	chr1:169881000-169888000	Weak transcription	Fetal Brain Male	brain
11	chr1:169881400-169901000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:169882200-169892000	Weak transcription	Brain Germinal Matrix	brain
13	chr1:169882800-169886800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:169883000-169886800	Weak transcription	Fetal Stomach	stomach
15	chr1:169883000-169890600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:169884200-169913000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:169884400-169888200	Weak transcription	Adipose Nuclei	Adipose
18	chr1:169884400-169889000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:169884400-169891000	Weak transcription	Esophagus	oesophagus
20	chr1:169884600-169887600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr1:169884600-169887800	Weak transcription	Small Intestine	intestine
22	chr1:169884600-169888400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:169884600-169888600	Weak transcription	NH-A	brain
24	chr1:169884600-169892800	Weak transcription	Pancreas	Pancrea
25	chr1:169884600-169895200	Weak transcription	Fetal Intestine Small	intestine
26	chr1:169884600-169900600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:169884600-169900600	Weak transcription	NHDF-Ad	bronchial
28	chr1:169885200-169886800	Weak transcription	Fetal Muscle Leg	muscle
29	chr1:169885200-169888200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:169885200-169888200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:169885200-169900800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:169885400-169894000	Weak transcription	Right Ventricle	heart
33	chr1:169885400-169913200	Weak transcription	Ovary	ovary
34	chr1:169885600-169892200	Weak transcription	Brain Substantia Nigra	brain
35	chr1:169885600-169903200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr1:169885800-169886800	Enhancers	GM12878-XiMat	blood
37	chr1:169885800-169896600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:169885800-169898000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:169886000-169894000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:169886200-169888200	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:169886400-169894600	Weak transcription	Primary B cells from cord blood	blood
42	chr1:169886400-169895200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:169886400-169913000	Weak transcription	Primary T cells fromperipheralblood	blood

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