Variant report

Variant	rs4520018
Chromosome Location	chr6:56611650-56611651
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56610420..56612281-chr6:56629163..56631061,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1599280	1.00[YRI][hapmap]
rs4413617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57183853	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57439200	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57936670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58912662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59493539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59643604	1.00[AFR][1000 genomes]
rs59801210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60143048	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60172134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60304191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60620079	1.00[AMR][1000 genomes]
rs60975519	1.00[AMR][1000 genomes]
rs61396940	0.91[AFR][1000 genomes]
rs7753074	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56592800-56611800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:56593200-56621200	Weak transcription	Fetal Muscle Leg	muscle
3	chr6:56605000-56613400	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr6:56605600-56614600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:56606600-56614000	Enhancers	Placenta Amnion	Placenta Amnion
6	chr6:56606600-56617600	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr6:56606800-56612400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:56607000-56612000	Weak transcription	Fetal Brain Female	brain
9	chr6:56607200-56614200	Weak transcription	Gastric	stomach
10	chr6:56607200-56618200	Weak transcription	Brain Germinal Matrix	brain
11	chr6:56607600-56612600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:56607600-56620600	Weak transcription	Fetal Intestine Small	intestine
13	chr6:56608000-56613800	Weak transcription	NH-A	brain
14	chr6:56608200-56614600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:56608200-56621000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:56608400-56614200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:56608400-56614600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:56608600-56614400	Weak transcription	NHDF-Ad	bronchial
19	chr6:56608600-56618000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:56609000-56612400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr6:56609200-56612600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:56609200-56617600	Enhancers	HMEC	breast
23	chr6:56609200-56619200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:56609600-56612000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:56609800-56614800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:56610000-56611800	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:56610000-56611800	Weak transcription	Fetal Heart	heart
28	chr6:56610000-56614000	Weak transcription	Stomach Mucosa	stomach
29	chr6:56610000-56614200	Weak transcription	NHLF	lung
30	chr6:56610200-56611800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr6:56610400-56611800	Weak transcription	Brain Hippocampus Middle	brain
32	chr6:56610400-56612400	Enhancers	Brain Substantia Nigra	brain
33	chr6:56610600-56612200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:56610600-56612600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:56610600-56614200	Enhancers	Muscle Satellite Cultured Cells	--
36	chr6:56610800-56612400	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr6:56610800-56612400	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr6:56610800-56612800	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr6:56610800-56613600	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr6:56611000-56612000	Enhancers	HSMM	muscle
41	chr6:56611000-56612400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:56611200-56612200	Enhancers	A549	lung
43	chr6:56611400-56611800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:56611400-56612000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr6:56611400-56612200	Enhancers	Placenta	Placenta
46	chr6:56611400-56612200	Enhancers	Psoas Muscle	Psoas
47	chr6:56611400-56612400	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr6:56611600-56611800	Enhancers	Esophagus	oesophagus
49	chr6:56611600-56611800	Flanking Active TSS	GM12878-XiMat	blood
50	chr6:56611600-56612000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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