Variant report

Variant	rs4413617
Chromosome Location	chr6:56610564-56610565
allele	C/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]
rs4520018	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:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56582600-56611600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:56592800-56611800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:56593200-56621200	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:56605000-56613400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr6:56605600-56611600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:56605600-56614600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:56606600-56614000	Enhancers	Placenta Amnion	Placenta Amnion
8	chr6:56606600-56617600	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr6:56606800-56611400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:56606800-56612400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:56607000-56612000	Weak transcription	Fetal Brain Female	brain
12	chr6:56607200-56610800	Weak transcription	Placenta	Placenta
13	chr6:56607200-56611600	Weak transcription	Left Ventricle	heart
14	chr6:56607200-56611600	Weak transcription	Right Atrium	heart
15	chr6:56607200-56611600	Weak transcription	Right Ventricle	heart
16	chr6:56607200-56614200	Weak transcription	Gastric	stomach
17	chr6:56607200-56618200	Weak transcription	Brain Germinal Matrix	brain
18	chr6:56607400-56611600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:56607600-56611600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:56607600-56611600	Weak transcription	HSMMtube	muscle
21	chr6:56607600-56612600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:56607600-56620600	Weak transcription	Fetal Intestine Small	intestine
23	chr6:56607800-56611600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:56607800-56611600	Enhancers	GM12878-XiMat	blood
25	chr6:56608000-56611600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:56608000-56613800	Weak transcription	NH-A	brain
27	chr6:56608200-56610600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr6:56608200-56614600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr6:56608200-56621000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr6:56608400-56611600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:56608400-56614200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr6:56608400-56614600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:56608600-56610600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:56608600-56611000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:56608600-56611600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:56608600-56611600	Weak transcription	HepG2	liver
37	chr6:56608600-56611600	Weak transcription	Osteobl	bone
38	chr6:56608600-56614400	Weak transcription	NHDF-Ad	bronchial
39	chr6:56608600-56618000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr6:56609000-56612400	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr6:56609200-56610800	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr6:56609200-56612600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:56609200-56617600	Enhancers	HMEC	breast
44	chr6:56609200-56619200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:56609400-56611600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr6:56609400-56611600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:56609400-56611600	Enhancers	NHEK	skin
48	chr6:56609600-56610800	Weak transcription	Psoas Muscle	Psoas
49	chr6:56609600-56611400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr6:56609600-56611600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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