Variant report

Variant	rs28705340
Chromosome Location	chr6:128826311-128826312
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LAMA2-2	chr6:128826270-128826325	ENSG00000227112.1

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10155795	0.99[AFR][1000 genomes]
rs13196432	0.88[EUR][1000 genomes]
rs13196790	0.97[AFR][1000 genomes]
rs13201242	0.96[AFR][1000 genomes]
rs13216847	0.99[AFR][1000 genomes]
rs1341598	0.92[EUR][1000 genomes]
rs28360647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28550449	0.99[AFR][1000 genomes]
rs34337200	0.96[AFR][1000 genomes]
rs34478800	0.92[EUR][1000 genomes]
rs34558551	0.87[AFR][1000 genomes]
rs34760929	0.96[AFR][1000 genomes]
rs34931647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35242805	0.96[AFR][1000 genomes]
rs35395689	0.99[AFR][1000 genomes]
rs35419289	0.96[AFR][1000 genomes]
rs36120502	0.99[AFR][1000 genomes]
rs58050191	0.97[AFR][1000 genomes]
rs6937769	0.81[EUR][1000 genomes]
rs71568906	0.99[AFR][1000 genomes]
rs7760626	0.97[AFR][1000 genomes]
rs9482888	0.93[AFR][1000 genomes]
rs9482890	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9491958	0.92[EUR][1000 genomes]
rs9491967	0.97[AFR][1000 genomes]
rs9491970	0.97[AFR][1000 genomes]
rs9491972	0.97[AFR][1000 genomes]
rs9491975	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv830800	chr6:128710631-128878435	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128808800-128830800	Weak transcription	Lung	lung
2	chr6:128813000-128828600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:128815200-128833800	Enhancers	Fetal Intestine Large	intestine
4	chr6:128816800-128826600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:128817200-128828600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:128817200-128839800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:128817200-128839800	Weak transcription	Aorta	Aorta
8	chr6:128819600-128827600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:128819800-128826600	Weak transcription	Brain Angular Gyrus	brain
10	chr6:128819800-128828600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr6:128819800-128828600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:128820600-128826600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr6:128820600-128833800	Enhancers	Fetal Intestine Small	intestine
14	chr6:128820800-128828400	Weak transcription	HSMMtube	muscle
15	chr6:128820800-128828600	Weak transcription	HSMM	muscle
16	chr6:128821200-128826800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:128821600-128836800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr6:128821800-128827000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr6:128821800-128827200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr6:128822000-128827000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:128822000-128828600	Weak transcription	Colonic Mucosa	Colon
22	chr6:128822200-128828600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:128822200-128828600	Weak transcription	Gastric	stomach
24	chr6:128822400-128828600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:128822800-128826600	Weak transcription	NHLF	lung
26	chr6:128823400-128832800	Enhancers	Stomach Mucosa	stomach
27	chr6:128823800-128826600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr6:128824000-128826600	Enhancers	Duodenum Mucosa	Duodenum
29	chr6:128824400-128828600	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr6:128824600-128827200	Enhancers	Brain Substantia Nigra	brain
31	chr6:128824800-128829400	Enhancers	Fetal Heart	heart
32	chr6:128825000-128827200	Enhancers	Fetal Stomach	stomach
33	chr6:128825000-128827800	Enhancers	Brain Anterior Caudate	brain
34	chr6:128825000-128829400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:128825200-128826800	Enhancers	A549	lung
36	chr6:128825200-128827400	Enhancers	Colon Smooth Muscle	Colon
37	chr6:128825400-128828600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:128825600-128826400	Enhancers	Right Atrium	heart
39	chr6:128825600-128827000	Enhancers	NHDF-Ad	bronchial
40	chr6:128825600-128827400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:128825600-128827400	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr6:128825600-128827400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:128825600-128827800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:128825600-128828600	Enhancers	Muscle Satellite Cultured Cells	--
45	chr6:128825800-128826800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr6:128825800-128826800	Weak transcription	Fetal Lung	lung
47	chr6:128825800-128827000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:128825800-128827200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr6:128825800-128828600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr6:128825800-128828600	Weak transcription	Small Intestine	intestine

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