Variant report

Variant	rs41267677
Chromosome Location	chr6:56727890-56727891
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	chr6:56726286..56729119-chr6:56729880..56733046,4	MCF-7	breast:
2	chr6:56725702..56727982-chr6:56732126..56734324,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BEND6-1	chr6:56727869-56728042	ENSG00000231441.1
2	lnc-BEND6-1	chr6:56727869-56728042	NONHSAT113249
3	lnc-BEND6-1	chr6:56727869-56728042	NONHSAT113250

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2967958	1.00[AMR][1000 genomes]
rs2967959	1.00[AMR][1000 genomes]
rs2967962	1.00[AMR][1000 genomes]
rs6928319	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7742007	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:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56717400-56730200	Weak transcription	Ovary	ovary
2	chr6:56717800-56730400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr6:56718200-56731000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:56721800-56731200	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:56723000-56732600	Weak transcription	Small Intestine	intestine
6	chr6:56724200-56733800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:56724600-56728000	Enhancers	HSMMtube	muscle
8	chr6:56724600-56728600	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr6:56724600-56730400	Enhancers	Fetal Intestine Small	intestine
10	chr6:56725000-56730400	Enhancers	HUVEC	blood vessel
11	chr6:56725200-56728600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:56725600-56730000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr6:56725600-56730200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:56725600-56731000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:56725600-56731200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:56725600-56734800	Enhancers	Hela-S3	cervix
17	chr6:56725800-56730400	Enhancers	Fetal Intestine Large	intestine
18	chr6:56726200-56728000	Genic enhancers	HSMM	muscle
19	chr6:56726600-56730000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr6:56727000-56729400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:56727000-56729800	Weak transcription	Colonic Mucosa	Colon
22	chr6:56727200-56728000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:56727200-56728000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:56727200-56728000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:56727200-56728000	Enhancers	Spleen	Spleen
26	chr6:56727200-56728000	Flanking Active TSS	NHDF-Ad	bronchial
27	chr6:56727200-56728200	Flanking Active TSS	Osteobl	bone
28	chr6:56727200-56728400	Enhancers	Left Ventricle	heart
29	chr6:56727200-56728400	Enhancers	Psoas Muscle	Psoas
30	chr6:56727200-56728600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:56727200-56728600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr6:56727200-56728800	Enhancers	Adipose Nuclei	Adipose
33	chr6:56727200-56729000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr6:56727200-56729200	Flanking Active TSS	A549	lung
35	chr6:56727200-56729400	Enhancers	Colon Smooth Muscle	Colon
36	chr6:56727200-56729400	Enhancers	NH-A	brain
37	chr6:56727200-56734600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:56727400-56728000	Enhancers	Brain Substantia Nigra	brain
39	chr6:56727400-56728200	Flanking Active TSS	NHLF	lung
40	chr6:56727400-56728800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:56727400-56729200	Enhancers	Placenta Amnion	Placenta Amnion
42	chr6:56727400-56730600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:56727400-56730600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr6:56727600-56728000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:56727600-56728000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:56727600-56728000	Enhancers	Stomach Mucosa	stomach
47	chr6:56727600-56728200	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr6:56727600-56728400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:56727600-56729400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:56727600-56730600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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