Variant report

Variant	rs28735880
Chromosome Location	chr18:12281812-12281813
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	chr18:12281440..12284374-chr18:12307536..12311164,3	K562	blood:
2	chr18:12280564..12282806-chr18:12308373..12310089,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CIDEA-4	chr18:12279426-12282738	NONHSAT058361

Variant related genes	Relation type
ENSG00000176014	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs7242157	1.00[AMR][1000 genomes]
rs9950263	1.00[AMR][1000 genomes]
rs9950494	1.00[AMR][1000 genomes]
rs9966548	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS 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 target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv909401	chr18:12211483-12312075	Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv909402	chr18:12211483-12325222	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv909403	chr18:12231060-12325222	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1061545	chr18:12235999-12328405	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer 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	30 gene(s)	inside rSNPs	diseases
8	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv870342	chr18:12270808-12295798	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1058661	chr18:12280366-12313865	Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12278200-12284200	Enhancers	Placenta Amnion	Placenta Amnion
2	chr18:12279200-12283000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr18:12279600-12284200	Enhancers	Placenta	Placenta
4	chr18:12279600-12287600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr18:12279800-12282200	Weak transcription	Hela-S3	cervix
6	chr18:12279800-12282400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr18:12279800-12282400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr18:12279800-12283000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr18:12279800-12283400	Enhancers	NHLF	lung
10	chr18:12279800-12284200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr18:12280000-12282000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr18:12280000-12282000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr18:12280000-12282200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr18:12280000-12282400	Weak transcription	HepG2	liver
15	chr18:12280000-12284000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr18:12280000-12287400	Weak transcription	Right Atrium	heart
17	chr18:12280000-12287800	Weak transcription	Ovary	ovary
18	chr18:12280400-12282400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr18:12280400-12282800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr18:12280400-12283000	Enhancers	Fetal Muscle Leg	muscle
21	chr18:12280400-12287400	Weak transcription	Adipose Nuclei	Adipose
22	chr18:12280400-12287600	Weak transcription	Aorta	Aorta
23	chr18:12280400-12287600	Weak transcription	Lung	lung
24	chr18:12280600-12282400	Enhancers	Fetal Muscle Trunk	muscle
25	chr18:12280800-12283000	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr18:12280800-12284400	Enhancers	Fetal Heart	heart
27	chr18:12281000-12282400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr18:12281000-12282800	Weak transcription	Fetal Stomach	stomach
29	chr18:12281200-12282200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr18:12281400-12283200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr18:12281400-12284600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr18:12281600-12282000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr18:12281600-12282200	Enhancers	HSMM	muscle
34	chr18:12281600-12282400	Enhancers	Muscle Satellite Cultured Cells	--
35	chr18:12281600-12282400	Enhancers	NHEK	skin
36	chr18:12281600-12282600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr18:12281600-12283000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr18:12281600-12283000	Enhancers	Right Ventricle	heart
39	chr18:12281600-12283200	Enhancers	Osteobl	bone
40	chr18:12281600-12283400	Enhancers	HMEC	breast
41	chr18:12281600-12283600	Enhancers	NHDF-Ad	bronchial
42	chr18:12281600-12284000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr18:12281600-12284000	Enhancers	HUVEC	blood vessel
44	chr18:12281800-12282400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr18:12281800-12282400	Enhancers	Colon Smooth Muscle	Colon
46	chr18:12281800-12282800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr18:12281800-12282800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr18:12281800-12283000	Flanking Active TSS	HSMMtube	muscle
49	chr18:12281800-12283000	Flanking Active TSS	NH-A	brain
50	chr18:12281800-12283200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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