Variant report

Variant	rs6594340
Chromosome Location	chr5:108195954-108195955
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:108193098..108195960-chr5:108197076..108199919,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10040696	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10044305	0.87[EUR][1000 genomes]
rs10060694	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10062204	0.85[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10063167	0.81[ASN][1000 genomes]
rs10079165	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10477431	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12153703	0.80[YRI][hapmap]
rs13180513	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2081126	0.88[EUR][1000 genomes]
rs2081129	0.90[EUR][1000 genomes]
rs2081130	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28637651	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2900035	0.84[EUR][1000 genomes]
rs34125469	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4604227	0.81[AMR][1000 genomes]
rs62360774	0.81[EUR][1000 genomes]
rs6594338	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6874229	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6875320	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6880284	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6889550	0.84[EUR][1000 genomes]
rs6891194	0.88[EUR][1000 genomes]
rs6895027	0.81[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7700630	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7709267	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7710482	0.84[EUR][1000 genomes]
rs7712834	0.85[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7712956	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs7725391	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7726708	0.86[EUR][1000 genomes]
rs7731891	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7735235	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9326747	0.86[EUR][1000 genomes]
rs9326748	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9885168	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv471039	chr5:108133967-108245089	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv1801555	chr5:108166720-108203055	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108147000-108198800	Weak transcription	Aorta	Aorta
2	chr5:108147000-108208800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:108166400-108203200	Weak transcription	HSMM	muscle
4	chr5:108166600-108217000	Weak transcription	Left Ventricle	heart
5	chr5:108167200-108220400	Weak transcription	Fetal Lung	lung
6	chr5:108168200-108203800	Weak transcription	Adipose Nuclei	Adipose
7	chr5:108169400-108229200	Weak transcription	Fetal Stomach	stomach
8	chr5:108173000-108199800	Weak transcription	Brain Angular Gyrus	brain
9	chr5:108173400-108239800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:108179800-108199800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:108179800-108202000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:108182000-108217000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:108183800-108260400	Weak transcription	Ovary	ovary
14	chr5:108187200-108202600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:108187200-108204600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:108187200-108211800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:108187800-108199200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:108190600-108200000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:108194000-108217000	Weak transcription	Esophagus	oesophagus
20	chr5:108194200-108203000	Weak transcription	NHLF	lung
21	chr5:108194600-108260000	Weak transcription	Fetal Intestine Large	intestine
22	chr5:108194800-108200000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr5:108194800-108204200	Weak transcription	NHEK	skin
24	chr5:108194800-108204600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr5:108194800-108207000	Weak transcription	HUVEC	blood vessel
26	chr5:108194800-108208600	Weak transcription	Osteobl	bone
27	chr5:108194800-108236200	Weak transcription	Hela-S3	cervix
28	chr5:108195000-108204800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr5:108195000-108211800	Weak transcription	NHDF-Ad	bronchial
30	chr5:108195200-108197600	Weak transcription	Fetal Brain Male	brain
31	chr5:108195200-108203400	Weak transcription	Primary B cells from cord blood	blood
32	chr5:108195200-108204800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr5:108195200-108206600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr5:108195200-108209000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:108195200-108211000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr5:108195200-108231600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr5:108195200-108231600	Weak transcription	Psoas Muscle	Psoas
38	chr5:108195200-108234400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr5:108195400-108202600	Weak transcription	Primary monocytes fromperipheralblood	blood

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