Variant report

Variant	rs11078405
Chromosome Location	chr17:17824978-17824979
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17822649..17827287-chr17:17828107..17833962,6	MCF-7	breast:
2	chr17:17822751..17824989-chr17:17833618..17835263,2	K562	blood:
3	chr17:17741927..17743549-chr17:17824784..17826455,2	MCF-7	breast:
4	chr17:17578891..17581684-chr17:17824075..17825729,2	K562	blood:
5	chr17:17722826..17725491-chr17:17823665..17826462,2	K562	blood:
6	chr17:17822871..17825553-chr17:17834729..17836696,2	MCF-7	breast:
7	chr17:17823331..17826317-chr17:17843856..17846226,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000072310	Chromatin interaction
ENSG00000223979	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10048206	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11078400	0.81[EUR][1000 genomes]
rs11078403	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11078404	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11078406	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11078407	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11078408	0.81[EUR][1000 genomes]
rs11650649	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11650890	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11656840	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11657074	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11657773	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11657845	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11658309	0.82[AMR][1000 genomes]
rs11869536	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11870660	0.81[EUR][1000 genomes]
rs11871899	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452219	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12452254	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12600546	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12603148	0.96[EUR][1000 genomes]
rs12936037	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12941039	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12943500	0.91[ASN][1000 genomes]
rs1889014	0.91[ASN][1000 genomes]
rs2350977	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28428991	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35451946	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4077198	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4077828	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4244602	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4257260	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4299203	0.81[EUR][1000 genomes]
rs4321247	0.91[EUR][1000 genomes]
rs4341796	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4343339	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4413022	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4414547	0.96[EUR][1000 genomes]
rs4470201	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4471742	0.81[EUR][1000 genomes]
rs4534911	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4553680	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616340	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4924823	0.80[EUR][1000 genomes]
rs4925123	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925125	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4925126	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4925129	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925130	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5002487	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57728924	0.81[EUR][1000 genomes]
rs62064156	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62064158	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62072049	0.84[EUR][1000 genomes]
rs6502619	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6502622	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6502624	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6502625	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502626	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6502627	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6502629	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66531105	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67253360	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7207043	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7207395	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208190	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7213225	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7214002	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7214536	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7219320	0.81[EUR][1000 genomes]
rs7222480	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7224815	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7503334	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8065416	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8065497	0.91[ASN][1000 genomes]
rs8065563	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8065970	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8066982	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8068175	0.81[EUR][1000 genomes]
rs8068820	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8070128	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8070624	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8070722	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8070748	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8073001	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8075965	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8076747	0.94[EUR][1000 genomes]
rs8077338	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8077530	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8078105	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8078138	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8078583	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8079321	0.81[EUR][1000 genomes]
rs8080061	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8080823	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs950966	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9635697	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9635698	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9890341	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9895750	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9904163	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9905284	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9907246	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9907287	0.81[EUR][1000 genomes]
rs9908017	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9908299	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9908832	0.94[EUR][1000 genomes]
rs9912895	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9913724	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9914127	0.81[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11078405	SREBF1	cis	Whole Blood	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17810800-17838400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr17:17811400-17838400	Weak transcription	Primary T cells from cord blood	blood
3	chr17:17814800-17833200	Weak transcription	Aorta	Aorta
4	chr17:17817600-17831600	Weak transcription	Fetal Brain Female	brain
5	chr17:17817800-17838200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr17:17820800-17826400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr17:17821000-17828400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr17:17821200-17829000	Enhancers	NHEK	skin
9	chr17:17821600-17827200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr17:17821800-17826400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr17:17821800-17827200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr17:17821800-17827200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr17:17821800-17828400	Enhancers	HMEC	breast
14	chr17:17822000-17826600	Enhancers	NHDF-Ad	bronchial
15	chr17:17822000-17827000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr17:17822000-17827200	Enhancers	Brain Hippocampus Middle	brain
17	chr17:17822000-17836600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr17:17822200-17826400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr17:17822200-17826600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr17:17822200-17826600	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr17:17822200-17827000	Enhancers	Brain Substantia Nigra	brain
22	chr17:17822400-17828400	Enhancers	NH-A	brain
23	chr17:17822600-17826800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr17:17823000-17825400	Weak transcription	Fetal Brain Male	brain
25	chr17:17823200-17838000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr17:17823200-17838200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr17:17823400-17825000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr17:17823400-17825600	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr17:17823400-17828200	Weak transcription	GM12878-XiMat	blood
30	chr17:17823400-17836400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr17:17823400-17838200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr17:17823600-17827800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr17:17823800-17826600	Enhancers	Brain Anterior Caudate	brain
34	chr17:17823800-17826600	Enhancers	Fetal Muscle Leg	muscle
35	chr17:17824000-17825200	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr17:17824000-17825200	Enhancers	Fetal Heart	heart
37	chr17:17824000-17825600	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr17:17824000-17826400	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr17:17824000-17826400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr17:17824000-17826400	Enhancers	Duodenum Mucosa	Duodenum
41	chr17:17824000-17826600	Enhancers	Placenta Amnion	Placenta Amnion
42	chr17:17824000-17826800	Enhancers	Liver	Liver
43	chr17:17824000-17827000	Enhancers	Brain Cingulate Gyrus	brain
44	chr17:17824000-17827000	Enhancers	Stomach Mucosa	stomach
45	chr17:17824000-17829200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr17:17824200-17825000	Flanking Active TSS	Hela-S3	cervix
47	chr17:17824200-17825600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr17:17824200-17826000	Flanking Active TSS	HepG2	liver
49	chr17:17824200-17826200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr17:17824200-17826400	Enhancers	H1 Cell Line	embryonic stem cell

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