Variant report

Variant	rs66531105
Chromosome Location	chr17:17809001-17809002
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17799113..17802641-chr17:17808261..17812088,4	K562	blood:
2	chr17:17732703..17734829-chr17:17808950..17811778,2	K562	blood:
3	chr17:17803950..17806140-chr17:17808249..17810276,3	MCF-7	breast:

Extended variants
information (count: 119 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10048206	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11078400	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11078403	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11078404	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11078405	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11078406	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078407	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078408	0.83[EUR][1000 genomes]
rs11650649	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11650890	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11656840	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11657074	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11657773	0.86[EUR][1000 genomes]
rs11657845	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11658309	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11869536	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870660	0.82[EUR][1000 genomes]
rs11871899	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12452219	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12452254	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12600546	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12603148	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12936037	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12941039	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16960744	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2350977	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28428991	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35451946	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4077198	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4077828	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244602	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4257260	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4299203	0.82[EUR][1000 genomes]
rs4321247	0.89[EUR][1000 genomes]
rs4341796	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4343339	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4413022	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4414547	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4470201	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4471742	0.83[EUR][1000 genomes]
rs4534911	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4553680	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4616340	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924822	0.81[AMR][1000 genomes]
rs4924823	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4925120	0.82[AMR][1000 genomes]
rs4925123	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4925125	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4925126	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925129	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4925130	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5002487	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57728924	0.82[EUR][1000 genomes]
rs62064156	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62064158	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072049	0.83[EUR][1000 genomes]
rs6502619	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6502622	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502624	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502625	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6502626	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6502627	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6502629	0.82[EUR][1000 genomes]
rs67253360	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207043	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7207395	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7208190	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7213225	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7214002	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7214536	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7219320	0.82[EUR][1000 genomes]
rs7222480	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7224815	0.83[EUR][1000 genomes]
rs7503334	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8065416	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8065563	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8065970	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8066982	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8068175	0.82[EUR][1000 genomes]
rs8068820	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8070128	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8070722	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8070748	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8073001	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8075965	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8076747	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8077338	0.81[EUR][1000 genomes]
rs8077530	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8078105	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8078138	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8078583	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8079321	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8080061	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8080823	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs950966	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9635697	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9635698	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9890341	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9895335	0.81[AMR][1000 genomes]
rs9895750	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9899634	0.80[AMR][1000 genomes]
rs9904163	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9905284	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9907246	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9907287	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9908017	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9908299	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9908832	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9911281	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9912895	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9913724	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9914127	0.83[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs66531105	SREBF1	cis	Whole Blood	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17781600-17810600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr17:17782200-17817000	Weak transcription	Fetal Kidney	kidney
3	chr17:17793000-17817200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr17:17797000-17817000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr17:17797600-17822400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr17:17801200-17817200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr17:17802400-17817000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr17:17802600-17817600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr17:17802600-17820000	Weak transcription	Primary B cells from cord blood	blood
10	chr17:17802600-17822400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr17:17802800-17812400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr17:17803000-17810200	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr17:17804600-17810000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr17:17804600-17810400	Weak transcription	Fetal Brain Male	brain
15	chr17:17804800-17810000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr17:17804800-17810400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr17:17804800-17814000	Weak transcription	Fetal Thymus	thymus
18	chr17:17804800-17814600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr17:17805000-17809800	Weak transcription	HUVEC	blood vessel
20	chr17:17805000-17810000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr17:17805000-17810000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr17:17805000-17810400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr17:17805000-17813400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr17:17805000-17817400	Weak transcription	Small Intestine	intestine
25	chr17:17805200-17809600	Weak transcription	Colon Smooth Muscle	Colon
26	chr17:17805200-17809600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr17:17805200-17809800	Weak transcription	Brain Anterior Caudate	brain
28	chr17:17805200-17809800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr17:17805200-17810000	Weak transcription	Colonic Mucosa	Colon
30	chr17:17805200-17810000	Strong transcription	Fetal Stomach	stomach
31	chr17:17805200-17810200	Weak transcription	NH-A	brain
32	chr17:17805600-17810400	Strong transcription	Thymus	Thymus
33	chr17:17806000-17809400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr17:17806000-17809800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr17:17806000-17810200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr17:17806000-17811400	Strong transcription	Primary T cells from cord blood	blood
37	chr17:17806000-17814400	Weak transcription	Stomach Mucosa	stomach
38	chr17:17806200-17810000	Weak transcription	HMEC	breast
39	chr17:17806400-17809800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr17:17806400-17809800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr17:17806400-17809800	Weak transcription	Right Atrium	heart
42	chr17:17806400-17810000	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr17:17806400-17810000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr17:17806400-17810000	Weak transcription	A549	lung
45	chr17:17806600-17809800	Weak transcription	Brain Substantia Nigra	brain
46	chr17:17806600-17810000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr17:17806600-17810000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr17:17806800-17809800	Strong transcription	Stomach Smooth Muscle	stomach
49	chr17:17807000-17810400	Strong transcription	Fetal Brain Female	brain
50	chr17:17807000-17810800	Enhancers	HepG2	liver

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