Variant report

Variant	rs3797896
Chromosome Location	chr5:80093800-80093801
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80092334..80094934-chr5:80095470..80097531,3	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1428030	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes]
rs1805355	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs1979005	0.85[ASN][1000 genomes]
rs2195291	0.82[CEU][hapmap]
rs3776969	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs3797877	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap]
rs3797885	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3797886	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3797897	0.87[ASN][1000 genomes]
rs3816729	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4703818	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704683	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4704686	0.85[ASN][1000 genomes]
rs4704687	0.85[ASN][1000 genomes]
rs58508689	0.87[ASN][1000 genomes]
rs6151628	0.82[CEU][hapmap]
rs6151639	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap]
rs6151705	0.81[AMR][1000 genomes]
rs6151714	0.83[AMR][1000 genomes]
rs6151769	0.84[AMR][1000 genomes]
rs6151789	0.81[AMR][1000 genomes]
rs6151826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151865	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151901	0.87[ASN][1000 genomes]
rs6879843	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881898	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6894961	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72765588	0.88[ASN][1000 genomes]
rs72765599	0.85[ASN][1000 genomes]
rs73125417	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7711890	0.83[AMR][1000 genomes]
rs7721000	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv882231	chr5:79984714-80187929	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1016100	chr5:80023679-80254194	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1021784	chr5:80023679-80313586	ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv537787	chr5:80023679-80313586	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 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	chr5:79971800-80112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:79985000-80100600	Weak transcription	Brain Germinal Matrix	brain
3	chr5:79998800-80109400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr5:80041200-80100400	Weak transcription	Gastric	stomach
5	chr5:80041800-80094200	Weak transcription	NHLF	lung
6	chr5:80042800-80118200	Weak transcription	Spleen	Spleen
7	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
8	chr5:80044000-80096400	Weak transcription	Brain Anterior Caudate	brain
9	chr5:80051600-80095000	Weak transcription	Psoas Muscle	Psoas
10	chr5:80052200-80095600	Weak transcription	Fetal Brain Male	brain
11	chr5:80057200-80094200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:80073400-80112800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:80075200-80114000	Weak transcription	Stomach Mucosa	stomach
14	chr5:80076200-80109600	Weak transcription	HepG2	liver
15	chr5:80077400-80108000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr5:80077600-80112000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:80077600-80118800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr5:80083000-80101400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr5:80083200-80098400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr5:80083800-80098800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr5:80085200-80127600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr5:80087400-80094400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr5:80087400-80132800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr5:80087800-80095200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr5:80087800-80167400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr5:80088200-80109600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr5:80088600-80095000	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr5:80089200-80093800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:80089200-80095200	Strong transcription	Fetal Stomach	stomach
30	chr5:80089400-80094200	Strong transcription	Esophagus	oesophagus
31	chr5:80089400-80110400	Weak transcription	Hela-S3	cervix
32	chr5:80089400-80118400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:80089400-80120200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:80089600-80100000	Weak transcription	HMEC	breast
35	chr5:80089600-80109200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr5:80089600-80110200	Weak transcription	Brain Angular Gyrus	brain
37	chr5:80089600-80118400	Weak transcription	NHEK	skin
38	chr5:80089800-80094000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr5:80089800-80112400	Weak transcription	K562	blood
40	chr5:80089800-80118400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr5:80090000-80109400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:80090000-80111000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr5:80090000-80118600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:80090200-80094000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr5:80090200-80109200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr5:80090200-80118400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr5:80090400-80094800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr5:80090400-80095600	Weak transcription	Colonic Mucosa	Colon
49	chr5:80090400-80098200	Weak transcription	Fetal Kidney	kidney
50	chr5:80090400-80124600	Weak transcription	Colon Smooth Muscle	Colon

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