Variant report

Variant	rs73404965
Chromosome Location	chr6:28565986-28565987
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28554693..28556296-chr6:28564365..28566355,2	K562	blood:
2	chr6:28564953..28566880-chr6:28649469..28651175,2	MCF-7	breast:
3	chr6:28553736..28559121-chr6:28563340..28566855,6	MCF-7	breast:
4	chr6:28554693..28558246-chr6:28562930..28566355,3	K562	blood:
5	chr6:28565424..28567496-chr6:28740751..28743719,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221191	Chromatin interaction
ENSG00000246350	Chromatin interaction
ENSG00000232040	Chromatin interaction

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

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

rs_ID	r²[population]
rs11753292	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11754112	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11754599	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11757235	0.82[ASN][1000 genomes]
rs11758822	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12110753	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12111360	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1319076	0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs28382587	0.82[ASN][1000 genomes]
rs2893967	0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs34211304	0.82[ASN][1000 genomes]
rs34560199	0.82[ASN][1000 genomes]
rs34668037	0.82[ASN][1000 genomes]
rs3886843	0.82[ASN][1000 genomes]
rs4435933	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56958518	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73391123	0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs73402976	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73402978	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73402982	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73402983	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73404961	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs73407134	0.88[AFR][1000 genomes]
rs73407157	0.92[AFR][1000 genomes]
rs73407159	0.92[AFR][1000 genomes]
rs73409121	0.94[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs73409125	0.82[ASN][1000 genomes]
rs73409140	0.94[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7738979	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7770993	0.88[AFR][1000 genomes]
rs7774808	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9791301	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[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	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28564800-28566200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr6:28564800-28566400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:28564800-28566400	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr6:28564800-28566400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr6:28564800-28566400	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr6:28564800-28566400	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr6:28565000-28566000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:28565000-28566000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:28565000-28566000	Active TSS	Right Atrium	heart
10	chr6:28565000-28566000	Active TSS	GM12878-XiMat	blood
11	chr6:28565000-28566200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:28565000-28566200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:28565000-28566200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:28565000-28566200	Bivalent/Poised TSS	Fetal Brain Female	brain
15	chr6:28565000-28566200	Active TSS	NHEK	skin
16	chr6:28565000-28566400	Active TSS	H1 Cell Line	embryonic stem cell
17	chr6:28565000-28566400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:28565000-28566400	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr6:28565000-28566400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:28565000-28566600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:28565000-28566800	Active TSS	Hela-S3	cervix
22	chr6:28565000-28567000	Active TSS	A549	lung
23	chr6:28565200-28566000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:28565200-28566000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:28565200-28566000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:28565200-28566000	Active TSS	Brain Hippocampus Middle	brain
27	chr6:28565200-28566000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr6:28565200-28566000	Bivalent/Poised TSS	Fetal Brain Male	brain
29	chr6:28565200-28566000	Active TSS	HSMM	muscle
30	chr6:28565200-28566000	Active TSS	HSMMtube	muscle
31	chr6:28565200-28566000	Active TSS	NHDF-Ad	bronchial
32	chr6:28565200-28566000	Active TSS	NHLF	lung
33	chr6:28565200-28566000	Active TSS	Osteobl	bone
34	chr6:28565200-28566200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr6:28565200-28566200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr6:28565200-28566200	Active TSS	Muscle Satellite Cultured Cells	--
37	chr6:28565200-28566200	Active TSS	Brain Anterior Caudate	brain
38	chr6:28565200-28566400	Active TSS	H9 Cell Line	embryonic stem cell
39	chr6:28565200-28566400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:28565200-28566400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:28565200-28566400	Active TSS	HMEC	breast
42	chr6:28565400-28566000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:28565400-28566000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:28565400-28566000	Active TSS	Adipose Nuclei	Adipose
45	chr6:28565400-28566000	Enhancers	Placenta Amnion	Placenta Amnion
46	chr6:28565600-28566000	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr6:28565600-28566000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
48	chr6:28565600-28566000	Bivalent Enhancer	Fetal Stomach	stomach
49	chr6:28565800-28566000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:28565800-28566000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast

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