Variant report

Variant	rs6999454
Chromosome Location	chr8:54658360-54658361
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:54652211..54654707-chr8:54657866..54660858,2	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1031979	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1031980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs10435587	1.00[CEU][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11994467	0.88[ASN][1000 genomes]
rs11996300	0.90[ASN][1000 genomes]
rs12056486	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12056719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.98[ASN][1000 genomes]
rs12234972	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13276766	0.86[ASN][1000 genomes]
rs1552148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16919507	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16919508	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes]
rs16919522	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16919534	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16919537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16919541	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16919563	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs16919571	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16919573	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1872063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.90[ASN][1000 genomes]
rs1905061	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2128150	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2170444	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2376011	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3735831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3757954	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs41321146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4236945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs4737192	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4737518	0.83[EUR][1000 genomes]
rs4737554	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4737558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4737753	1.00[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs4737761	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs4737764	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs4737765	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4737821	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4737974	1.00[CEU][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes]
rs4738025	1.00[CEU][hapmap]
rs4738027	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4738470	0.86[ASN][1000 genomes]
rs4738646	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4738701	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4738884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4738916	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55682919	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55876329	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55964335	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56818292	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56956173	0.83[EUR][1000 genomes]
rs56973376	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57550901	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58473841	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58558817	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58970885	0.83[EUR][1000 genomes]
rs61070518	0.88[ASN][1000 genomes]
rs6473893	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs6984257	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6986372	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6987427	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6988009	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6988082	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6988808	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs6988812	0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6994851	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs6997003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6997127	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7005696	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs7006934	0.85[CEU][hapmap];0.81[CHB][hapmap];0.93[EUR][1000 genomes]
rs7009705	0.83[EUR][1000 genomes]
rs7018162	1.00[CEU][hapmap];0.82[YRI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73587624	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73587627	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73680321	0.83[EUR][1000 genomes]
rs73682549	1.00[EUR][1000 genomes]
rs73682551	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73682552	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73682555	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73682568	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73682570	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7387704	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7843701	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs900163	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs958268	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs9643480	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9643819	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9643820	1.00[CEU][hapmap];0.92[ASN][1000 genomes]

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	esv2758159	chr8:54474589-54737473	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv2759616	chr8:54474589-54737473	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1021775	chr8:54631303-54827173	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv539621	chr8:54631303-54827173	Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:54627400-54663400	Weak transcription	Hela-S3	cervix
2	chr8:54635000-54660200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr8:54642600-54672800	Weak transcription	Right Ventricle	heart
4	chr8:54645600-54671400	Weak transcription	NHLF	lung
5	chr8:54646000-54672600	Weak transcription	Psoas Muscle	Psoas
6	chr8:54647200-54666600	Weak transcription	Brain Substantia Nigra	brain
7	chr8:54647600-54661600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr8:54647600-54666600	Weak transcription	A549	lung
9	chr8:54648600-54667200	Weak transcription	HSMMtube	muscle
10	chr8:54650200-54661000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr8:54650200-54661200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr8:54650200-54661400	Weak transcription	Stomach Mucosa	stomach
13	chr8:54650200-54663400	Weak transcription	Brain Germinal Matrix	brain
14	chr8:54650200-54671000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr8:54650200-54707400	Weak transcription	HUVEC	blood vessel
16	chr8:54651200-54658400	Strong transcription	Primary B cells from cord blood	blood
17	chr8:54651400-54663200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr8:54651400-54670400	Weak transcription	Fetal Brain Male	brain
19	chr8:54651600-54658600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr8:54652600-54660000	Weak transcription	Fetal Intestine Small	intestine
21	chr8:54652800-54673000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr8:54653400-54670000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr8:54654200-54658400	Strong transcription	Fetal Intestine Large	intestine
24	chr8:54654200-54658600	Strong transcription	Primary T cells from cord blood	blood
25	chr8:54654200-54658600	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr8:54654400-54658400	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr8:54654400-54658600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr8:54654400-54658800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr8:54654400-54661600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr8:54654800-54661600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr8:54655400-54662400	Weak transcription	NH-A	brain
32	chr8:54655400-54663400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr8:54655400-54669600	Weak transcription	Esophagus	oesophagus
34	chr8:54655400-54703600	Weak transcription	Brain Angular Gyrus	brain
35	chr8:54655600-54661600	Weak transcription	K562	blood
36	chr8:54655600-54662200	Weak transcription	Fetal Kidney	kidney
37	chr8:54655600-54662400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr8:54655600-54663000	Weak transcription	Fetal Lung	lung
39	chr8:54655600-54665600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr8:54655600-54666800	Weak transcription	Brain Hippocampus Middle	brain
41	chr8:54655600-54666800	Weak transcription	Fetal Muscle Trunk	muscle
42	chr8:54655600-54667000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr8:54655600-54672400	Weak transcription	Fetal Heart	heart
44	chr8:54655800-54661800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr8:54655800-54671000	Weak transcription	Fetal Brain Female	brain
46	chr8:54655800-54726000	Weak transcription	Colonic Mucosa	Colon
47	chr8:54656200-54659600	Weak transcription	NHDF-Ad	bronchial
48	chr8:54656200-54662200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr8:54656200-54666400	Weak transcription	Placenta	Placenta
50	chr8:54656200-54666800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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