Variant report

Variant	rs13098588
Chromosome Location	chr3:20127585-20127586
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:20114096..20116899-chr3:20125846..20128363,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11713069	1.00[ASN][1000 genomes]
rs13066876	1.00[ASN][1000 genomes]
rs13066923	1.00[ASN][1000 genomes]
rs13069629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095743	1.00[ASN][1000 genomes]
rs13096876	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097157	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097409	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17627750	0.83[ASN][1000 genomes]
rs17627906	0.83[ASN][1000 genomes]
rs17627936	0.83[ASN][1000 genomes]
rs17678713	0.83[ASN][1000 genomes]
rs17796904	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17804451	1.00[ASN][1000 genomes]
rs34204839	1.00[ASN][1000 genomes]
rs34515517	1.00[ASN][1000 genomes]
rs34572705	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35424474	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35632245	1.00[ASN][1000 genomes]
rs35645247	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35659955	1.00[ASN][1000 genomes]
rs35776229	1.00[ASN][1000 genomes]
rs35841175	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36029475	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3960789	1.00[ASN][1000 genomes]
rs41285061	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241545	1.00[ASN][1000 genomes]
rs4858156	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858171	1.00[ASN][1000 genomes]
rs4858751	1.00[ASN][1000 genomes]
rs4858752	1.00[ASN][1000 genomes]
rs4858755	1.00[ASN][1000 genomes]
rs4858763	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858765	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858768	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55812129	0.83[ASN][1000 genomes]
rs71316246	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71316248	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71316249	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv433359	chr3:20090908-20587572	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv470450	chr3:20096735-20389045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv1001006	chr3:20110743-20752628	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv536512	chr3:20110743-20752628	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
12	esv1829018	chr3:20116077-20596244	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
13	esv1827700	chr3:20119716-20489086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
14	esv1830036	chr3:20121828-20278275	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
15	esv1830599	chr3:20121828-20375643	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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 miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13098588	SGOL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20102800-20136800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr3:20106800-20130800	Weak transcription	Fetal Intestine Large	intestine
3	chr3:20108200-20127600	Weak transcription	Ovary	ovary
4	chr3:20116400-20194800	Weak transcription	NHDF-Ad	bronchial
5	chr3:20117200-20130800	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr3:20118800-20129200	Weak transcription	Fetal Lung	lung
7	chr3:20122800-20131000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:20123000-20127600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr3:20123000-20127800	Weak transcription	Right Atrium	heart
10	chr3:20123000-20131000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:20123000-20131600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:20123000-20137000	Weak transcription	Spleen	Spleen
13	chr3:20123000-20138400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:20123000-20140800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:20123000-20153000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:20123200-20127600	Weak transcription	Lung	lung
17	chr3:20123200-20129400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:20123200-20129400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:20123200-20129400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:20123200-20130200	Weak transcription	Fetal Muscle Leg	muscle
21	chr3:20123200-20131000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:20123200-20131000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:20123200-20131000	Weak transcription	Adipose Nuclei	Adipose
24	chr3:20123200-20131000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:20123200-20131000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:20123200-20131000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:20123200-20131200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr3:20123200-20131200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr3:20123200-20131600	Weak transcription	Brain Substantia Nigra	brain
30	chr3:20123200-20132400	Weak transcription	Liver	Liver
31	chr3:20123200-20132800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:20123200-20136800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:20123200-20136800	Weak transcription	Brain Angular Gyrus	brain
34	chr3:20123200-20136800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:20123200-20137000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr3:20123200-20137200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:20123200-20137200	Weak transcription	Esophagus	oesophagus
38	chr3:20123200-20137200	Weak transcription	Fetal Heart	heart
39	chr3:20123200-20137200	Weak transcription	Left Ventricle	heart
40	chr3:20123200-20137200	Weak transcription	Psoas Muscle	Psoas
41	chr3:20123200-20137200	Weak transcription	Right Ventricle	heart
42	chr3:20123200-20137400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:20123200-20137400	Weak transcription	Gastric	stomach
44	chr3:20123200-20137400	Weak transcription	Pancreas	Pancrea
45	chr3:20123200-20138600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:20123200-20141000	Weak transcription	Stomach Mucosa	stomach
47	chr3:20123200-20153200	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr3:20125400-20129200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:20126000-20131000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:20126400-20128600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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