Variant report

Variant	rs1080368
Chromosome Location	chr7:17719753-17719754
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs17138105	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2723549	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887761	chr7:16834361-17732490	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv887762	chr7:16834361-17746628	Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv887763	chr7:16834361-17750811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv887765	chr7:16839835-17750811	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1015831	chr7:16854300-17732227	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv538750	chr7:16854300-17732227	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv1023604	chr7:16964718-17732630	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv538752	chr7:16964718-17732630	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers 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	25 gene(s)	inside rSNPs	diseases
9	nsv1018747	chr7:17074137-17732771	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv538753	chr7:17074137-17732771	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
11	nsv464399	chr7:17085939-17755584	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
12	nsv606343	chr7:17085939-17755584	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
13	nsv887790	chr7:17228122-17746628	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised 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	21 gene(s)	inside rSNPs	diseases
14	nsv887791	chr7:17228122-17750811	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS 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	21 gene(s)	inside rSNPs	diseases
15	nsv869352	chr7:17237983-17932878	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
16	nsv1021524	chr7:17251148-17963307	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
17	nsv1021289	chr7:17254117-17873816	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
18	nsv538754	chr7:17254117-17873816	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
19	nsv534309	chr7:17254118-17932878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
20	nsv533938	chr7:17254118-18040301	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
21	nsv1022647	chr7:17425895-17731397	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
22	nsv887804	chr7:17571140-17885468	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
23	nsv1024398	chr7:17630148-18545073	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
24	nsv538764	chr7:17630148-18545073	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
25	nsv1023105	chr7:17702135-17733754	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
26	nsv1031163	chr7:17707971-17733754	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1080368	NIPA1	cis	Frontal Cortex	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:17713000-17722000	Enhancers	HMEC	breast
2	chr7:17714000-17720800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr7:17716400-17723400	Enhancers	NHLF	lung
4	chr7:17717000-17722600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr7:17717200-17721000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:17717200-17722600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr7:17717400-17722600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr7:17717600-17720000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:17717800-17720800	Weak transcription	Fetal Lung	lung
10	chr7:17718400-17722000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr7:17718400-17723600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr7:17718800-17722800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:17719000-17719800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:17719000-17720400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:17719200-17719800	Enhancers	H1 Cell Line	embryonic stem cell
16	chr7:17719200-17719800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:17719200-17719800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr7:17719200-17719800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:17719200-17719800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr7:17719200-17719800	Enhancers	Brain Anterior Caudate	brain
21	chr7:17719200-17719800	Active TSS	Brain Hippocampus Middle	brain
22	chr7:17719200-17719800	Enhancers	Esophagus	oesophagus
23	chr7:17719200-17719800	Enhancers	Fetal Muscle Trunk	muscle
24	chr7:17719200-17719800	Enhancers	Fetal Muscle Leg	muscle
25	chr7:17719200-17719800	Enhancers	Placenta	Placenta
26	chr7:17719200-17719800	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr7:17719200-17719800	Enhancers	Small Intestine	intestine
28	chr7:17719200-17719800	Flanking Active TSS	HSMM	muscle
29	chr7:17719200-17720000	Enhancers	Right Atrium	heart
30	chr7:17719200-17720000	Flanking Active TSS	HSMMtube	muscle
31	chr7:17719200-17720200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr7:17719200-17720200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr7:17719200-17720200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr7:17719200-17720200	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr7:17719200-17720200	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr7:17719200-17720200	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr7:17719200-17720200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr7:17719200-17720200	Enhancers	Ovary	ovary
39	chr7:17719200-17720200	Flanking Active TSS	Osteobl	bone
40	chr7:17719200-17720400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr7:17719200-17720600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:17719200-17720600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr7:17719200-17720800	Enhancers	Hela-S3	cervix
44	chr7:17719200-17721000	Enhancers	Adipose Nuclei	Adipose
45	chr7:17719200-17723000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr7:17719400-17719800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr7:17719400-17719800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr7:17719400-17719800	Enhancers	Colon Smooth Muscle	Colon
49	chr7:17719400-17719800	Enhancers	Placenta Amnion	Placenta Amnion
50	chr7:17719400-17719800	Enhancers	Spleen	Spleen

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