Variant report

Variant	rs12965296
Chromosome Location	chr18:8244875-8244876
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12953765	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12962826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12963007	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964764	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs34816086	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4130758	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6506561	0.88[TSI][hapmap]
rs6506566	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs7232952	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs7504663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv458018	chr18:8110805-8645907	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv576426	chr18:8110805-8645907	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1057288	chr18:8218725-8351340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv543639	chr18:8218725-8351340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1055995	chr18:8222469-8271135	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12965296	FAM38B	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:8191200-8288600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr18:8211600-8265000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr18:8217800-8257800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr18:8227000-8253200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr18:8227200-8255000	Weak transcription	A549	lung
6	chr18:8227400-8254000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr18:8230200-8254200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr18:8231400-8245000	Weak transcription	Ovary	ovary
9	chr18:8231400-8265000	Weak transcription	Pancreas	Pancrea
10	chr18:8231600-8247600	Weak transcription	Adipose Nuclei	Adipose
11	chr18:8233200-8253200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr18:8235000-8260400	Weak transcription	Psoas Muscle	Psoas
13	chr18:8239600-8253200	Weak transcription	Right Ventricle	heart
14	chr18:8239600-8264000	Weak transcription	HepG2	liver
15	chr18:8240400-8247600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr18:8241200-8263600	Weak transcription	Fetal Lung	lung
17	chr18:8242200-8245000	Weak transcription	Fetal Stomach	stomach
18	chr18:8242200-8252000	Weak transcription	Colon Smooth Muscle	Colon
19	chr18:8242200-8252400	Weak transcription	Fetal Brain Female	brain
20	chr18:8242400-8245200	Weak transcription	Brain Anterior Caudate	brain
21	chr18:8242400-8247800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr18:8242400-8254800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr18:8242400-8260600	Weak transcription	Brain Hippocampus Middle	brain
24	chr18:8242400-8261000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr18:8242400-8264000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr18:8242600-8251000	Weak transcription	Brain Substantia Nigra	brain
27	chr18:8242600-8253000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr18:8242600-8254000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr18:8242600-8260600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr18:8243400-8263000	Weak transcription	Gastric	stomach
31	chr18:8243800-8245000	Strong transcription	Left Ventricle	heart
32	chr18:8243800-8245600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr18:8243800-8252800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr18:8244000-8260400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr18:8244200-8245200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr18:8244400-8245200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr18:8244400-8255600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr18:8244600-8245200	Strong transcription	Fetal Thymus	thymus
39	chr18:8244600-8245400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr18:8244600-8245400	Strong transcription	Aorta	Aorta
41	chr18:8244600-8245400	Strong transcription	Fetal Muscle Leg	muscle
42	chr18:8244600-8254600	Weak transcription	Liver	Liver
43	chr18:8244800-8245200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr18:8244800-8245400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr18:8244800-8245600	Strong transcription	Thymus	Thymus
46	chr18:8244800-8248000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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