Variant report

Variant	rs62072049
Chromosome Location	chr17:17906520-17906521
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17904155..17906615-chr17:17908063..17910293,2	K562	blood:
2	chr17:17739486..17742070-chr17:17906240..17907771,2	K562	blood:
3	chr17:17903006..17906615-chr17:17908063..17910293,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATPAF2-1	chr17:17906236-17906554	NONHSAT146130

Variant related genes	Relation type
ENSG00000072310	Chromatin interaction
ENSG00000171962	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10048206	0.84[EUR][1000 genomes]
rs11078400	0.85[EUR][1000 genomes]
rs11078404	0.82[EUR][1000 genomes]
rs11078405	0.84[EUR][1000 genomes]
rs11078406	0.83[EUR][1000 genomes]
rs11078407	0.83[EUR][1000 genomes]
rs11652894	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11656840	0.83[EUR][1000 genomes]
rs11657074	0.87[EUR][1000 genomes]
rs11658309	0.82[EUR][1000 genomes]
rs11869536	0.83[EUR][1000 genomes]
rs11871899	0.85[EUR][1000 genomes]
rs12150369	0.84[EUR][1000 genomes]
rs12452219	0.84[EUR][1000 genomes]
rs12452254	0.85[EUR][1000 genomes]
rs12600546	0.83[EUR][1000 genomes]
rs12603148	0.84[EUR][1000 genomes]
rs12936037	0.87[EUR][1000 genomes]
rs12941039	0.87[EUR][1000 genomes]
rs12948749	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28428991	0.83[EUR][1000 genomes]
rs28537385	0.82[EUR][1000 genomes]
rs2955371	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2955377	0.81[EUR][1000 genomes]
rs2955378	0.81[EUR][1000 genomes]
rs2955382	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35451946	0.85[EUR][1000 genomes]
rs4077198	0.83[EUR][1000 genomes]
rs4077828	0.83[EUR][1000 genomes]
rs4244602	0.85[EUR][1000 genomes]
rs4257260	0.84[EUR][1000 genomes]
rs4321247	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4341796	0.85[EUR][1000 genomes]
rs4343339	0.84[EUR][1000 genomes]
rs4365348	0.84[EUR][1000 genomes]
rs4413022	0.84[EUR][1000 genomes]
rs4414547	0.84[EUR][1000 genomes]
rs4459604	0.83[EUR][1000 genomes]
rs4470201	0.83[EUR][1000 genomes]
rs4506969	0.82[EUR][1000 genomes]
rs4534911	0.85[EUR][1000 genomes]
rs4553680	0.86[EUR][1000 genomes]
rs4584886	0.82[EUR][1000 genomes]
rs4616340	0.84[EUR][1000 genomes]
rs4924823	0.84[EUR][1000 genomes]
rs4924832	0.82[EUR][1000 genomes]
rs4925129	0.85[EUR][1000 genomes]
rs4925130	0.82[EUR][1000 genomes]
rs5002487	0.85[EUR][1000 genomes]
rs62064156	0.85[EUR][1000 genomes]
rs62064158	0.82[EUR][1000 genomes]
rs62072050	0.82[EUR][1000 genomes]
rs6502622	0.83[EUR][1000 genomes]
rs6502624	0.83[EUR][1000 genomes]
rs6502626	0.83[EUR][1000 genomes]
rs6502627	0.83[EUR][1000 genomes]
rs6502631	0.82[EUR][1000 genomes]
rs6502632	0.84[EUR][1000 genomes]
rs66531105	0.83[EUR][1000 genomes]
rs67253360	0.83[EUR][1000 genomes]
rs7207043	0.81[EUR][1000 genomes]
rs7207395	0.85[EUR][1000 genomes]
rs7207821	0.82[EUR][1000 genomes]
rs7209003	0.83[EUR][1000 genomes]
rs7212167	0.84[EUR][1000 genomes]
rs7213225	0.84[EUR][1000 genomes]
rs7214002	0.83[EUR][1000 genomes]
rs7214536	0.83[EUR][1000 genomes]
rs7215524	0.81[EUR][1000 genomes]
rs7222480	0.85[EUR][1000 genomes]
rs7223696	0.83[EUR][1000 genomes]
rs8065416	0.84[EUR][1000 genomes]
rs8065970	0.84[EUR][1000 genomes]
rs8066982	0.83[EUR][1000 genomes]
rs8068820	0.82[EUR][1000 genomes]
rs8069811	0.83[EUR][1000 genomes]
rs8070128	0.81[EUR][1000 genomes]
rs8070722	0.82[EUR][1000 genomes]
rs8070748	0.84[EUR][1000 genomes]
rs8073001	0.83[EUR][1000 genomes]
rs8075189	0.83[EUR][1000 genomes]
rs8076747	0.80[EUR][1000 genomes]
rs8077530	0.80[EUR][1000 genomes]
rs8078105	0.80[EUR][1000 genomes]
rs8078138	0.84[EUR][1000 genomes]
rs8078583	0.84[EUR][1000 genomes]
rs8079321	0.85[EUR][1000 genomes]
rs8079418	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8080061	0.85[EUR][1000 genomes]
rs8080823	0.86[EUR][1000 genomes]
rs9635697	0.84[EUR][1000 genomes]
rs9635698	0.83[EUR][1000 genomes]
rs9890341	0.83[EUR][1000 genomes]
rs9895750	0.86[EUR][1000 genomes]
rs9896837	0.81[EUR][1000 genomes]
rs9897761	0.84[EUR][1000 genomes]
rs9904163	0.83[EUR][1000 genomes]
rs9905284	0.84[EUR][1000 genomes]
rs9907246	0.87[EUR][1000 genomes]
rs9907287	0.85[EUR][1000 genomes]
rs9908017	0.85[EUR][1000 genomes]
rs9908299	0.86[EUR][1000 genomes]
rs9908832	0.83[EUR][1000 genomes]
rs9911281	0.83[EUR][1000 genomes]
rs9911850	0.83[EUR][1000 genomes]
rs9912096	0.83[EUR][1000 genomes]
rs9912895	0.83[EUR][1000 genomes]
rs9913277	0.83[EUR][1000 genomes]
rs9913724	0.82[EUR][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	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv907766	chr17:17682484-17957348	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
5	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats 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	13 gene(s)	inside rSNPs	diseases
6	nsv510701	chr17:17850474-17955485	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62072049	SREBF1	cis	Whole Blood	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17876600-17914600	Weak transcription	Aorta	Aorta
2	chr17:17876800-17909400	Weak transcription	Brain Substantia Nigra	brain
3	chr17:17876800-17912000	Weak transcription	Colon Smooth Muscle	Colon
4	chr17:17881800-17908200	Weak transcription	Pancreas	Pancrea
5	chr17:17886800-17909400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr17:17886800-17913000	Weak transcription	Fetal Lung	lung
7	chr17:17889000-17907400	Weak transcription	Brain Anterior Caudate	brain
8	chr17:17890000-17907400	Weak transcription	Brain Germinal Matrix	brain
9	chr17:17892200-17908400	Weak transcription	Lung	lung
10	chr17:17892400-17910800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr17:17892600-17909800	Weak transcription	Brain Angular Gyrus	brain
12	chr17:17892800-17908000	Weak transcription	Spleen	Spleen
13	chr17:17894000-17920600	Weak transcription	Stomach Mucosa	stomach
14	chr17:17894600-17911400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr17:17895200-17909600	Weak transcription	NHLF	lung
16	chr17:17898000-17909200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr17:17898000-17910800	Weak transcription	Brain Hippocampus Middle	brain
18	chr17:17898200-17908200	Weak transcription	Right Ventricle	heart
19	chr17:17898200-17908400	Weak transcription	Fetal Brain Female	brain
20	chr17:17898200-17909000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr17:17898200-17918000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr17:17898200-17918000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr17:17898400-17907400	Weak transcription	Fetal Muscle Leg	muscle
24	chr17:17898400-17910000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr17:17898400-17911400	Weak transcription	HSMM	muscle
26	chr17:17898600-17908400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr17:17898600-17909800	Weak transcription	Adipose Nuclei	Adipose
28	chr17:17898600-17909800	Weak transcription	Ovary	ovary
29	chr17:17898600-17910600	Weak transcription	Placenta	Placenta
30	chr17:17898600-17910800	Weak transcription	Esophagus	oesophagus
31	chr17:17898600-17917600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr17:17898800-17908800	Weak transcription	NHEK	skin
33	chr17:17901200-17908200	Weak transcription	Fetal Stomach	stomach
34	chr17:17901200-17909200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr17:17901600-17907400	Weak transcription	Left Ventricle	heart
36	chr17:17902200-17907400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr17:17903000-17907400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr17:17903000-17911400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:17903200-17909800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr17:17903400-17907400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr17:17903400-17907400	Weak transcription	Fetal Heart	heart
42	chr17:17903400-17907600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr17:17903400-17909600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr17:17903400-17909800	Weak transcription	Liver	Liver
45	chr17:17903600-17907400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr17:17903600-17907400	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr17:17903600-17908800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr17:17903600-17913200	Weak transcription	Gastric	stomach
49	chr17:17903600-17913600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr17:17903800-17909800	Weak transcription	Duodenum Mucosa	Duodenum

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