Variant report

Variant	rs17494145
Chromosome Location	chr1:113547342-113547343
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HNF4A	chr1:113546898-113547359	HepG2	liver:	n/a	chr1:113547144-113547159 chr1:113547096-113547108 chr1:113546947-113546962 chr1:113547095-113547108 chr1:113547146-113547159 chr1:113547145-113547157 chr1:113547146-113547158 chr1:113547146-113547158 chr1:113547146-113547158 chr1:113547095-113547110 chr1:113546948-113546956 chr1:113547095-113547109 chr1:113547095-113547110 chr1:113547095-113547110 chr1:113547143-113547161 chr1:113547096-113547108 chr1:113547096-113547109 chr1:113547146-113547159 chr1:113547146-113547159 chr1:113547145-113547159 chr1:113547145-113547158
2	MYBL2	chr1:113546682-113547349	HepG2	liver:	n/a	n/a
3	FOXA1	chr1:113546758-113547441	HepG2	liver:	n/a	chr1:113547013-113547025
4	EP300	chr1:113546693-113547359	HepG2	liver:	n/a	chr1:113547012-113547022 chr1:113547030-113547044
5	FOXA2	chr1:113546815-113547345	HepG2	liver:	n/a	chr1:113547013-113547025
6	NR2F2	chr1:113546603-113547365	HepG2	liver:	n/a	chr1:113547142-113547157
7	FOXA1	chr1:113546753-113547442	HepG2	liver:	n/a	chr1:113547013-113547025
8	FOXA1	chr1:113546647-113547394	HepG2	liver:	n/a	chr1:113547013-113547025
9	HNF4A	chr1:113546624-113547384	HepG2	liver:	n/a	chr1:113547144-113547159 chr1:113547096-113547108 chr1:113546947-113546962 chr1:113547095-113547108 chr1:113547146-113547159 chr1:113547145-113547157 chr1:113547146-113547158 chr1:113547146-113547158 chr1:113547146-113547158 chr1:113547095-113547110 chr1:113546948-113546956 chr1:113547095-113547109 chr1:113547095-113547110 chr1:113547095-113547110 chr1:113547143-113547161 chr1:113547096-113547108 chr1:113547096-113547109 chr1:113547146-113547159 chr1:113547146-113547159 chr1:113547145-113547159 chr1:113547145-113547158
10	EP300	chr1:113546684-113547368	HepG2	liver:	n/a	chr1:113547012-113547022 chr1:113547030-113547044
11	FOXA1	chr1:113546691-113547385	HepG2	liver:	n/a	chr1:113547013-113547025
12	NFIC	chr1:113546686-113547408	HepG2	liver:	n/a	n/a
13	FOXA2	chr1:113546570-113547373	HepG2	liver:	n/a	chr1:113547013-113547025
14	ARID3A	chr1:113546711-113547347	HepG2	liver:	n/a	n/a
15	TEAD4	chr1:113546769-113547412	HepG2	liver:	n/a	n/a
16	HNF4G	chr1:113546646-113547389	HepG2	liver:	n/a	chr1:113547096-113547108 chr1:113546947-113546962 chr1:113547095-113547108 chr1:113547146-113547159 chr1:113547145-113547157 chr1:113547146-113547158 chr1:113547146-113547158 chr1:113547146-113547158 chr1:113547095-113547110 chr1:113546948-113546956 chr1:113547095-113547109 chr1:113547095-113547110 chr1:113547095-113547110 chr1:113547143-113547161 chr1:113547096-113547108 chr1:113547096-113547109 chr1:113547146-113547159 chr1:113547146-113547159 chr1:113547145-113547159 chr1:113547145-113547158
17	HDAC2	chr1:113546779-113547396	HepG2	liver:	n/a	chr1:113547013-113547022 chr1:113547026-113547040 chr1:113547027-113547041 chr1:113547030-113547044 chr1:113547025-113547039 chr1:113547034-113547048 chr1:113546881-113546889 chr1:113547029-113547043
18	SP1	chr1:113546548-113547488	HepG2	liver:	n/a	n/a
19	RXRA	chr1:113546577-113547350	HepG2	liver:	n/a	chr1:113547093-113547112 chr1:113547095-113547108 chr1:113547095-113547108 chr1:113547146-113547160 chr1:113547146-113547159 chr1:113547094-113547108 chr1:113547146-113547159 chr1:113547095-113547108 chr1:113547142-113547162 chr1:113547145-113547154 chr1:113547092-113547112 chr1:113547146-113547159
20	HDAC2	chr1:113546785-113547394	HepG2	liver:	n/a	chr1:113547013-113547022 chr1:113547026-113547040 chr1:113547027-113547041 chr1:113547030-113547044 chr1:113547025-113547039 chr1:113547034-113547048 chr1:113546881-113546889 chr1:113547029-113547043
21	NR2F2	chr1:113546598-113547456	HepG2	liver:	n/a	chr1:113547142-113547157
22	MAX	chr1:113546670-113547483	HepG2	liver:	n/a	n/a
23	MYBL2	chr1:113546634-113547456	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000236066	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12064292	0.81[EUR][1000 genomes]
rs1216778	0.95[EUR][1000 genomes]
rs17440299	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17493313	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs17494180	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2149036	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28556822	0.81[EUR][1000 genomes]
rs3849174	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4838971	0.81[EUR][1000 genomes]
rs4839270	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4839272	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839276	0.91[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839277	0.90[EUR][1000 genomes]
rs55768060	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55982206	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55992320	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56007797	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56019044	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669006	0.95[EUR][1000 genomes]
rs66899043	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72683432	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72683434	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72683442	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72683453	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72683454	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72683459	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72683463	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72683468	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7518984	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs7524567	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536532	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs7542229	0.82[EUR][1000 genomes]
rs7545602	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7550843	0.91[CEU][hapmap]
rs7552903	0.91[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429505	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs9429709	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs9429710	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv1004102	chr1:113295805-113551210	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
10	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
11	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
12	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17494145	SLC16A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113511200-113558000	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr1:113511200-113558600	Weak transcription	NHDF-Ad	bronchial
3	chr1:113511200-113564000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:113526600-113564200	Weak transcription	Placenta	Placenta
5	chr1:113526800-113558600	Weak transcription	GM12878-XiMat	blood
6	chr1:113528200-113556600	Weak transcription	Small Intestine	intestine
7	chr1:113529000-113554400	Weak transcription	Lung	lung
8	chr1:113533600-113555600	Weak transcription	Fetal Lung	lung
9	chr1:113534400-113548400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr1:113535600-113549200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:113535600-113552200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:113535600-113557000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:113535800-113550600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:113535800-113564000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:113535800-113564000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:113535800-113564200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:113535800-113568800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:113537200-113554800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:113537400-113550400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:113537400-113554200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:113537600-113552800	Weak transcription	Fetal Thymus	thymus
22	chr1:113538600-113558600	Weak transcription	Spleen	Spleen
23	chr1:113539600-113564200	Weak transcription	Brain Germinal Matrix	brain
24	chr1:113541000-113573800	Weak transcription	Right Ventricle	heart
25	chr1:113541400-113550200	Weak transcription	Primary B cells from cord blood	blood
26	chr1:113541400-113553200	Weak transcription	Aorta	Aorta
27	chr1:113541400-113554800	Weak transcription	A549	lung
28	chr1:113541600-113551400	Weak transcription	NH-A	brain
29	chr1:113541600-113555600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:113541600-113564200	Weak transcription	Osteobl	bone
31	chr1:113541800-113550000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:113541800-113552200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:113541800-113552800	Weak transcription	Ovary	ovary
34	chr1:113541800-113554800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:113541800-113554800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:113541800-113564000	Weak transcription	K562	blood
37	chr1:113542000-113549800	Weak transcription	Primary T cells from cord blood	blood
38	chr1:113542000-113550000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:113542000-113550000	Weak transcription	Brain Anterior Caudate	brain
40	chr1:113542000-113551000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:113542000-113552200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:113542000-113552800	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:113542000-113554000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:113542000-113554400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr1:113542000-113558400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr1:113542000-113564000	Weak transcription	Hela-S3	cervix
47	chr1:113542200-113549200	Weak transcription	Brain Angular Gyrus	brain
48	chr1:113542200-113550000	Weak transcription	Left Ventricle	heart
49	chr1:113542200-113550400	Weak transcription	Fetal Muscle Leg	muscle
50	chr1:113542200-113550600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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