Variant report

Variant	rs9904163
Chromosome Location	chr17:17830553-17830554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17827704..17830573-chr17:17832977..17835399,2	K562	blood:
2	chr17:17830467..17833990-chr17:17840176..17843911,4	MCF-7	breast:
3	chr17:17822649..17827287-chr17:17828107..17833962,6	MCF-7	breast:

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10048206	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11078400	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11078403	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11078404	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11078405	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11078406	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078407	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078408	0.83[EUR][1000 genomes]
rs11650649	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11650890	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11656840	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11657074	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11657773	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11657845	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11658309	0.85[AMR][1000 genomes]
rs11869536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870660	0.82[EUR][1000 genomes]
rs11871899	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12452219	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12452254	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12600546	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12603148	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12936037	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12941039	0.81[EUR][1000 genomes]
rs16960744	0.82[AMR][1000 genomes]
rs2350977	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28428991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35451946	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4077198	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4077828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244602	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4257260	0.85[AFR][1000 genomes];0.91[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	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4343339	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4413022	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4414547	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4470201	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4471742	0.83[EUR][1000 genomes]
rs4534911	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4553680	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4616340	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924823	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4925120	0.80[AMR][1000 genomes]
rs4925123	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4925125	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4925126	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925129	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4925130	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5002487	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57728924	0.82[EUR][1000 genomes]
rs62064156	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62064158	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62072049	0.83[EUR][1000 genomes]
rs6502619	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6502622	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502624	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502625	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6502626	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6502627	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6502629	0.82[EUR][1000 genomes]
rs66531105	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67253360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207043	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7207395	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7208190	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7213225	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7214002	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7214536	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7219320	0.82[EUR][1000 genomes]
rs7222480	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7224815	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7503334	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8065416	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8065563	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8065970	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8066982	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8068175	0.82[EUR][1000 genomes]
rs8068820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8070128	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8070722	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8070748	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8073001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8075965	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8076747	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8077338	0.81[EUR][1000 genomes]
rs8077530	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8078105	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8078138	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8078583	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8079321	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8080061	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8080823	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs950966	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9635697	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9635698	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9890341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9895750	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9905284	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9907246	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9907287	0.83[EUR][1000 genomes]
rs9908017	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9908299	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9908832	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9911281	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9912895	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9913724	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9914127	0.83[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
rs9904163	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	chr17:17810800-17838400	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	chr17:17822000-17836600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr17:17823200-17838000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr17:17823200-17838200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr17:17823400-17836400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr17:17823400-17838200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr17:17824600-17831200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr17:17824800-17838200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr17:17825000-17837600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr17:17826000-17831000	Weak transcription	Esophagus	oesophagus
15	chr17:17826000-17832400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr17:17826200-17831600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr17:17826200-17833600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr17:17826200-17837800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr17:17826200-17838400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr17:17826200-17838400	Weak transcription	Small Intestine	intestine
21	chr17:17826400-17830600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr17:17826400-17830600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:17826400-17831400	Weak transcription	Brain Germinal Matrix	brain
24	chr17:17826400-17831600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr17:17826400-17831600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr17:17826400-17831600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr17:17826400-17831600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr17:17826400-17831600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr17:17826400-17831600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr17:17826400-17831600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr17:17826400-17831600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr17:17826400-17831600	Weak transcription	HUVEC	blood vessel
33	chr17:17826400-17831800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr17:17826400-17831800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr17:17826400-17831800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr17:17826400-17831800	Weak transcription	Spleen	Spleen
37	chr17:17826400-17832000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr17:17826400-17832000	Weak transcription	Adipose Nuclei	Adipose
39	chr17:17826400-17833000	Weak transcription	Fetal Kidney	kidney
40	chr17:17826600-17830600	Weak transcription	Fetal Muscle Leg	muscle
41	chr17:17826600-17831600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr17:17826600-17831800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr17:17826600-17832000	Weak transcription	Placenta	Placenta
44	chr17:17826600-17834400	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr17:17826600-17838000	Weak transcription	Hela-S3	cervix
46	chr17:17827000-17831600	Enhancers	HSMM	muscle
47	chr17:17827000-17831800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr17:17827000-17838400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr17:17827200-17840400	Weak transcription	Colon Smooth Muscle	Colon
50	chr17:17828000-17835200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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