Variant report

Variant	rs9948485
Chromosome Location	chr18:7815373-7815374
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRRC30-4	chr18:7814116-7815728	ENSG00000264596.1

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs16952564	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs16952566	0.82[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs28478569	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28611041	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4356548	0.83[ASN][1000 genomes]
rs4572487	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs59483663	0.86[ASN][1000 genomes]
rs7244492	0.83[ASN][1000 genomes]
rs727952	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs9951957	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv458016	chr18:7488133-7934001	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv576399	chr18:7488133-7934001	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2762810	chr18:7492090-7924728	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv576425	chr18:7747873-7859757	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1062454	chr18:7784432-7838015	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7810200-7817600	Weak transcription	Ovary	ovary
2	chr18:7810200-7822400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr18:7810200-7824200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr18:7812600-7816400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr18:7813200-7815400	ZNF genes & repeats	Fetal Lung	lung
6	chr18:7813200-7822600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr18:7813400-7815600	ZNF genes & repeats	Thymus	Thymus
8	chr18:7813400-7816000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr18:7814000-7815400	ZNF genes & repeats	A549	lung
10	chr18:7814000-7815600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr18:7814000-7815600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr18:7814000-7815800	ZNF genes & repeats	Fetal Stomach	stomach
13	chr18:7814000-7816000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr18:7814200-7815400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr18:7814200-7815400	ZNF genes & repeats	Liver	Liver
16	chr18:7814200-7815600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
17	chr18:7814200-7815600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr18:7814200-7815600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr18:7814400-7815400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr18:7814400-7815400	ZNF genes & repeats	Left Ventricle	heart
21	chr18:7814400-7815400	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
22	chr18:7814600-7815800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr18:7814600-7821400	Weak transcription	Fetal Heart	heart
24	chr18:7815200-7815400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr18:7815200-7815400	ZNF genes & repeats	Psoas Muscle	Psoas
26	chr18:7815200-7815400	ZNF genes & repeats	Right Ventricle	heart
27	chr18:7815200-7815400	ZNF genes & repeats	Stomach Smooth Muscle	stomach

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