Variant report

Variant	rs3777646
Chromosome Location	chr6:54200785-54200786
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:54177292..54179184-chr6:54200767..54202415,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10080851	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17755505	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17828461	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17828521	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736352	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3736353	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822894	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41413844	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55868486	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56257351	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57614124	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57677324	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58204168	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58555206	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58969244	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59502546	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60299436	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61162221	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67321849	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6902402	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6907037	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6926710	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6927886	0.81[EUR][1000 genomes]
rs72959309	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72965255	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7746042	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9395950	0.81[ASN][1000 genomes]
rs9464069	0.85[ASN][1000 genomes]
rs9474821	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9474827	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9474829	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9474831	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs949469	0.87[EUR][1000 genomes];0.98[ASN][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	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv885888	chr6:54132353-54266032	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54198800-54201000	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr6:54198800-54202200	Enhancers	HUVEC	blood vessel
3	chr6:54199200-54200800	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr6:54199600-54201000	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr6:54200000-54201000	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr6:54200000-54201600	Enhancers	A549	lung
7	chr6:54200000-54201600	Enhancers	NH-A	brain
8	chr6:54200200-54201000	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr6:54200200-54201000	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr6:54200200-54201200	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr6:54200200-54201200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:54200200-54201200	Enhancers	Hela-S3	cervix
13	chr6:54200200-54201400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:54200200-54201400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:54200200-54201400	Enhancers	HMEC	breast
16	chr6:54200200-54201400	Enhancers	HSMM	muscle
17	chr6:54200200-54201400	Enhancers	NHEK	skin
18	chr6:54200200-54201600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:54200200-54201600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:54200400-54200800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:54200400-54201200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:54200400-54201200	Enhancers	HSMMtube	muscle
23	chr6:54200400-54201400	Enhancers	NHDF-Ad	bronchial
24	chr6:54200400-54201400	Enhancers	NHLF	lung
25	chr6:54200400-54201400	Enhancers	Osteobl	bone
26	chr6:54200400-54201600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:54200600-54201000	Enhancers	H1 Cell Line	embryonic stem cell
28	chr6:54200600-54201000	Enhancers	H9 Cell Line	embryonic stem cell
29	chr6:54200600-54201000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:54200600-54201000	Enhancers	Colon Smooth Muscle	Colon
31	chr6:54200600-54201000	Enhancers	Placenta Amnion	Placenta Amnion
32	chr6:54200600-54201000	Enhancers	Rectal Smooth Muscle	rectum
33	chr6:54200600-54201000	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr6:54200600-54201400	Enhancers	Muscle Satellite Cultured Cells	--

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