Variant report

Variant	rs11078403
Chromosome Location	chr17:17803416-17803417
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17744210..17746760-chr17:17803236..17805554,2	MCF-7	breast:
2	chr17:17584391..17586114-chr17:17802672..17804501,2	MCF-7	breast:
3	chr17:17742976..17745476-chr17:17800458..17803422,2	K562	blood:

Variant related genes	Relation type
ENSG00000108557	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10048206	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1052299	0.80[AMR][1000 genomes]
rs11078400	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11078404	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11078405	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11078406	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11078407	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11650649	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11650890	0.93[EUR][1000 genomes]
rs11656840	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11657074	0.83[EUR][1000 genomes]
rs11657845	0.83[EUR][1000 genomes]
rs11658309	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11869536	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11871899	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12452219	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12452254	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12600546	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12603148	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12936037	0.83[EUR][1000 genomes]
rs12938501	0.80[AMR][1000 genomes]
rs12941039	0.82[EUR][1000 genomes]
rs2236513	0.82[AMR][1000 genomes]
rs2350977	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28428991	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3183702	0.82[AMR][1000 genomes]
rs35451946	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3744115	0.80[AMR][1000 genomes]
rs4077198	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4077828	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4244602	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4257260	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4321247	0.84[EUR][1000 genomes]
rs4341796	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4343339	0.90[EUR][1000 genomes]
rs4413022	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4414547	0.91[EUR][1000 genomes]
rs4470201	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4534911	0.91[EUR][1000 genomes]
rs4553680	0.90[EUR][1000 genomes]
rs4616340	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4924822	0.85[AMR][1000 genomes]
rs4924823	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4925119	0.81[AMR][1000 genomes]
rs4925123	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4925125	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4925126	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925129	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4925130	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5002487	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62064156	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62064158	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6502619	0.93[EUR][1000 genomes]
rs6502622	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6502624	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6502625	0.83[EUR][1000 genomes]
rs6502626	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6502627	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66531105	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67253360	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7207043	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7207395	0.91[EUR][1000 genomes]
rs7208190	0.90[EUR][1000 genomes]
rs7213225	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7214002	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7214536	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7222480	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7503334	0.93[EUR][1000 genomes]
rs8065416	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8065563	0.93[EUR][1000 genomes]
rs8065970	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8066982	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8068820	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8070128	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8070722	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8070748	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8073001	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8075965	0.88[EUR][1000 genomes]
rs8076747	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8077530	0.89[EUR][1000 genomes]
rs8078105	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8078138	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8078583	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8079321	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8080061	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8080823	0.90[EUR][1000 genomes]
rs950966	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9635697	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9635698	0.90[EUR][1000 genomes]
rs9890341	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9893690	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9895750	0.82[EUR][1000 genomes]
rs9902941	0.80[AMR][1000 genomes]
rs9904163	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9905284	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9907246	0.83[EUR][1000 genomes]
rs9907287	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9908017	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9908299	0.82[EUR][1000 genomes]
rs9908832	0.89[EUR][1000 genomes]
rs9911281	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9912895	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9913724	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9915776	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11078403	SREBF1	cis	Whole Blood	GTEx
rs11078403	AC122129.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17767600-17807400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr17:17769200-17804600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr17:17781600-17810600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr17:17782200-17803800	Weak transcription	Stomach Mucosa	stomach
5	chr17:17782200-17817000	Weak transcription	Fetal Kidney	kidney
6	chr17:17783000-17808200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr17:17790200-17803800	Strong transcription	Fetal Intestine Small	intestine
8	chr17:17792600-17803600	Weak transcription	HUVEC	blood vessel
9	chr17:17792600-17803800	Strong transcription	Fetal Stomach	stomach
10	chr17:17793000-17803800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr17:17793000-17817200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr17:17795000-17806400	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr17:17795600-17804600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr17:17796600-17805000	Strong transcription	Primary T cells from cord blood	blood
15	chr17:17797000-17817000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr17:17797600-17822400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr17:17797800-17803800	Weak transcription	Fetal Brain Male	brain
18	chr17:17799400-17803800	Weak transcription	NH-A	brain
19	chr17:17800200-17804200	Weak transcription	Fetal Thymus	thymus
20	chr17:17800400-17803800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr17:17800400-17803800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr17:17800400-17803800	Weak transcription	Pancreas	Pancrea
23	chr17:17800400-17804000	Weak transcription	Aorta	Aorta
24	chr17:17800400-17804000	Weak transcription	Brain Angular Gyrus	brain
25	chr17:17800400-17804000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr17:17800400-17804000	Weak transcription	Right Ventricle	heart
27	chr17:17800400-17804800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr17:17800600-17803800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr17:17800600-17803800	Weak transcription	Brain Substantia Nigra	brain
30	chr17:17800600-17804000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr17:17800800-17807800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr17:17801200-17817200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr17:17801800-17804000	Weak transcription	Small Intestine	intestine
34	chr17:17801800-17805000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr17:17802000-17803600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr17:17802000-17803600	Weak transcription	Spleen	Spleen
37	chr17:17802000-17803800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr17:17802000-17803800	Weak transcription	Left Ventricle	heart
39	chr17:17802000-17803800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr17:17802000-17803800	Weak transcription	NHLF	lung
41	chr17:17802000-17804000	Weak transcription	Psoas Muscle	Psoas
42	chr17:17802000-17805800	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr17:17802200-17803600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr17:17802200-17803600	Weak transcription	NHEK	skin
45	chr17:17802200-17803800	Weak transcription	Brain Germinal Matrix	brain
46	chr17:17802200-17803800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr17:17802200-17803800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr17:17802200-17804000	Weak transcription	Esophagus	oesophagus
49	chr17:17802200-17804000	Weak transcription	Fetal Intestine Large	intestine
50	chr17:17802400-17803600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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