Variant report

Variant	rs11728880
Chromosome Location	chr4:152280898-152280899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10024721	0.82[EUR][1000 genomes]
rs10471070	0.82[EUR][1000 genomes]
rs11099806	0.82[EUR][1000 genomes]
rs11099807	0.82[EUR][1000 genomes]
rs12503602	0.89[EUR][1000 genomes]
rs2407171	0.82[EUR][1000 genomes]
rs2897618	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4455397	0.80[EUR][1000 genomes]
rs4696079	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696080	0.83[EUR][1000 genomes]
rs4696249	0.82[EUR][1000 genomes]
rs4696250	0.82[EUR][1000 genomes]
rs4696251	0.82[EUR][1000 genomes]
rs4696256	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6810430	0.82[EUR][1000 genomes]
rs6831644	0.88[EUR][1000 genomes]
rs6844259	0.85[EUR][1000 genomes]
rs7435680	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7678653	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7692939	0.82[EUR][1000 genomes]
rs9991859	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1025192	chr4:152202627-152498890	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537307	chr4:152202627-152498890	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv880624	chr4:152280646-152549112	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11728880	FAM160A1	cis	Whole Blood	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152269800-152281000	Weak transcription	Fetal Intestine Small	intestine
2	chr4:152275600-152282000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:152278000-152281200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:152278600-152281000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:152278600-152281400	Enhancers	Brain Anterior Caudate	brain
6	chr4:152278600-152281600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:152278600-152282600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr4:152278800-152281600	Enhancers	Brain Substantia Nigra	brain
9	chr4:152279800-152281000	Enhancers	Brain Cingulate Gyrus	brain
10	chr4:152279800-152281200	Enhancers	Fetal Brain Male	brain
11	chr4:152279800-152281400	Enhancers	Brain Angular Gyrus	brain
12	chr4:152279800-152281400	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr4:152279800-152281800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:152279800-152283600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:152279800-152283800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:152280000-152281200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:152280600-152281400	Enhancers	Fetal Lung	lung
18	chr4:152280600-152281600	Enhancers	Brain Germinal Matrix	brain
19	chr4:152280600-152281600	Enhancers	Brain Hippocampus Middle	brain
20	chr4:152280600-152281600	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr4:152280800-152281000	Enhancers	Right Atrium	heart
22	chr4:152280800-152281000	Enhancers	HepG2	liver
23	chr4:152280800-152281200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:152280800-152281200	Enhancers	Fetal Heart	heart
25	chr4:152280800-152281200	Enhancers	Fetal Muscle Leg	muscle
26	chr4:152280800-152281200	Enhancers	Lung	lung
27	chr4:152280800-152281200	Enhancers	Pancreas	Pancrea
28	chr4:152280800-152281200	Enhancers	HUVEC	blood vessel
29	chr4:152280800-152281600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr4:152280800-152281600	Enhancers	Duodenum Mucosa	Duodenum
31	chr4:152280800-152281600	Enhancers	Right Ventricle	heart

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