Variant report

Variant	rs55754640
Chromosome Location	chr6:4959028-4959029
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	chr6:4950081..4953438-chr6:4957036..4959775,3	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs17285248	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17356490	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1033905	chr6:4955826-5080904	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4943600-4959600	Weak transcription	NHDF-Ad	bronchial
2	chr6:4943600-4970000	Weak transcription	Psoas Muscle	Psoas
3	chr6:4946200-4970800	Weak transcription	Fetal Brain Female	brain
4	chr6:4947600-4970600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:4949200-4965200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:4949600-4960800	Weak transcription	Brain Germinal Matrix	brain
7	chr6:4949800-4960000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:4954400-4959600	Weak transcription	Fetal Intestine Large	intestine
9	chr6:4954400-4961600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:4954400-4967200	Weak transcription	Gastric	stomach
11	chr6:4954600-4961000	Weak transcription	HepG2	liver
12	chr6:4954600-4961800	Weak transcription	NHLF	lung
13	chr6:4954600-4964600	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:4954800-4965200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:4954800-4973800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:4955000-4965800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:4956400-4959200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:4956400-4959400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:4956400-4964600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr6:4956400-4964800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:4956600-4959400	Weak transcription	Primary T cells from cord blood	blood
22	chr6:4956600-4965000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:4956600-4965400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:4956600-4965400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:4956800-4959400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:4956800-4960000	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr6:4956800-4960400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:4956800-4965200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:4956800-4965200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:4956800-4965400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr6:4956800-4968000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:4956800-4970800	Weak transcription	HSMMtube	muscle
33	chr6:4957000-4965200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr6:4957000-4970800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:4957200-4959400	Weak transcription	Fetal Intestine Small	intestine
36	chr6:4957200-4961600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:4957200-4964600	Weak transcription	Fetal Stomach	stomach
38	chr6:4957400-4959800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:4957600-4960400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:4958400-4959200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
41	chr6:4958400-4961800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:4958400-4965000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:4958400-4973800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr6:4958600-4964400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:4959000-4959200	Enhancers	HSMM	muscle

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