Variant report

Variant	rs1543555
Chromosome Location	chr6:5033791-5033792
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	chr6:5032382..5034589-chr6:5044699..5046553,2	MCF-7	breast:
2	chr6:3924356..3927289-chr6:5032549..5034643,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPP40-1	chr6:5031990-5034916	ENSG00000248284

Variant related genes	Relation type
ENSG00000252419	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1536056	1.00[AFR][1000 genomes]
rs1539001	1.00[AFR][1000 genomes]
rs1592033	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
7	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription 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	23 gene(s)	inside rSNPs	diseases
9	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5027000-5036400	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr6:5027200-5034600	Weak transcription	Fetal Thymus	thymus
3	chr6:5027200-5047200	Weak transcription	Adipose Nuclei	Adipose
4	chr6:5029400-5034200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:5030600-5034200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:5031000-5034400	Weak transcription	Osteobl	bone
7	chr6:5031200-5034000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr6:5031200-5034200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:5031200-5042800	Weak transcription	Ovary	ovary
10	chr6:5031400-5036400	Weak transcription	K562	blood
11	chr6:5031600-5034000	Weak transcription	Fetal Muscle Leg	muscle
12	chr6:5031600-5034200	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr6:5031600-5034200	Weak transcription	Primary B cells from peripheral blood	blood
14	chr6:5031600-5042800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr6:5031800-5034200	Weak transcription	Thymus	Thymus
16	chr6:5031800-5043800	Weak transcription	Spleen	Spleen
17	chr6:5032600-5034000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:5032600-5035400	Enhancers	HepG2	liver
19	chr6:5032800-5034400	Enhancers	Fetal Stomach	stomach
20	chr6:5032800-5037200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:5033000-5033800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:5033000-5034000	Enhancers	HMEC	breast
23	chr6:5033000-5034200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr6:5033000-5034200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:5033000-5034400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:5033000-5035000	Enhancers	Fetal Muscle Trunk	muscle
27	chr6:5033000-5035800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr6:5033000-5035800	Enhancers	Placenta	Placenta
29	chr6:5033000-5036000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:5033200-5033800	Active TSS	Esophagus	oesophagus
31	chr6:5033400-5033800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr6:5033400-5033800	Weak transcription	Fetal Lung	lung
33	chr6:5033400-5033800	Enhancers	A549	lung
34	chr6:5033400-5034200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:5033400-5034200	Weak transcription	NHDF-Ad	bronchial
36	chr6:5033400-5034600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr6:5033400-5035800	Enhancers	NHEK	skin
38	chr6:5033400-5036400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr6:5033400-5036600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:5033400-5036600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:5033400-5036800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:5033400-5046000	Weak transcription	Fetal Intestine Small	intestine
43	chr6:5033400-5048600	Weak transcription	Aorta	Aorta
44	chr6:5033600-5033800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr6:5033600-5034200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:5033600-5034400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr6:5033600-5034600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:5033600-5035800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:5033600-5036000	Enhancers	Primary hematopoietic stem cells	blood

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