Variant report

Variant	rs13222805
Chromosome Location	chr7:19958855-19958856
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MACC1-1	chr7:19958604-19958883	ENSG00000243004.1
2	lnc-MACC1-1	chr7:19958615-19958883	ENSG00000243004.1
3	lnc-MACC1-1	chr7:19958823-19958883	ENSG00000243004.1
4	lnc-MACC1-1	chr7:19958602-19958883	NONHSAT119395
5	lnc-MACC1-1	chr7:19958604-19958883	NR_110114

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs13233581	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238182	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13240921	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17142207	0.81[EUR][1000 genomes]
rs17453222	0.85[EUR][1000 genomes]
rs34232728	0.81[EUR][1000 genomes]
rs34315480	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34359299	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34811148	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34976267	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36191174	0.81[EUR][1000 genomes]
rs36198836	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6953958	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6955046	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6968110	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73072750	0.82[AMR][1000 genomes];0.89[EUR][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	nsv1018601	chr7:19272360-20008881	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1033223	chr7:19682192-20461375	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv538795	chr7:19682192-20461375	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	esv1847477	chr7:19778086-19970584	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv887826	chr7:19816240-20033899	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv1844137	chr7:19862221-19970584	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
7	nsv887828	chr7:19874391-19959826	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
8	nsv887829	chr7:19876806-19959826	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
9	nsv1027445	chr7:19947297-20211733	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13222805	SP8	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:19951200-19959800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:19952000-19960000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr7:19954800-19973000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr7:19956000-19959400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr7:19956000-19959400	Weak transcription	HSMM	muscle
6	chr7:19956200-19959000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr7:19956200-19959400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr7:19956200-19960200	Weak transcription	NH-A	brain
9	chr7:19956400-19988000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr7:19958400-19960400	Enhancers	NHEK	skin
11	chr7:19958600-19959000	Flanking Active TSS	HUVEC	blood vessel
12	chr7:19958600-19960000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:19958600-19960800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr7:19958600-19961200	Enhancers	Fetal Lung	lung
15	chr7:19958800-19959000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:19958800-19959000	Enhancers	HMEC	breast
17	chr7:19958800-19959200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr7:19958800-19959400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr7:19958800-19959400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr7:19958800-19960000	Enhancers	Fetal Stomach	stomach

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