Variant report

Variant	rs6603952
Chromosome Location	chr1:77992361-77992362
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	chr1:77991832..77994057-chr1:78008305..78010332,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1013399	0.82[ASN][1000 genomes]
rs10782654	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10873949	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11162362	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11162363	0.80[EUR][1000 genomes]
rs11162364	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12071212	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12074409	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12095064	0.80[ASN][1000 genomes]
rs1565850	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1976334	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2133202	0.80[AFR][1000 genomes]
rs2647486	0.80[ASN][1000 genomes]
rs2647487	0.81[ASN][1000 genomes]
rs2803136	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2803168	0.80[ASN][1000 genomes]
rs3738079	0.80[ASN][1000 genomes]
rs3767032	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3767033	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4589153	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4600093	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4949657	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4949658	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4949659	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4949808	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6692369	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs6695989	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs6696083	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7545544	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7551211	0.80[ASN][1000 genomes]
rs7551729	0.80[ASN][1000 genomes]
rs9787153	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[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	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv871143	chr1:77955577-78031994	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1533	chr1:77990504-78036279	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77980800-77999400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:77981800-77998400	Weak transcription	Osteobl	bone
3	chr1:77981800-77999200	Weak transcription	NHLF	lung
4	chr1:77981800-77999400	Weak transcription	HSMMtube	muscle
5	chr1:77982000-77998200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:77982000-77998200	Weak transcription	Brain Angular Gyrus	brain
7	chr1:77982200-77998200	Weak transcription	Brain Anterior Caudate	brain
8	chr1:77983000-78009200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:77984600-77996400	Strong transcription	NHDF-Ad	bronchial
10	chr1:77985200-77999400	Weak transcription	Brain Substantia Nigra	brain
11	chr1:77985400-77999800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:77987600-77993200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:77988400-77999800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:77988600-77999400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:77988800-77992600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:77989000-77998200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:77990400-77998200	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:77991200-77993200	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr1:77991400-77995600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:77991400-77996200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:77991400-77996400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:77992000-77993000	Weak transcription	HSMM	muscle
23	chr1:77992000-77998400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr1:77992000-77999000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr1:77992000-77999200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:77992000-77999200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr1:77992000-77999200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:77992200-77993000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:77992200-77999200	Weak transcription	Primary T cells from cord blood	blood
30	chr1:77992200-77999200	Weak transcription	Primary T cells fromperipheralblood	blood

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