Variant report

Variant	rs13069629
Chromosome Location	chr3:20138262-20138263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:19986031..19988662-chr3:20137303..20140134,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163576	Chromatin interaction
ENSG00000144566	Chromatin interaction

Extended variants
information (count: 55 )
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]
rs13095743	1.00[ASN][1000 genomes]
rs13096876	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097157	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097409	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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];0.92[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];0.92[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];0.92[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:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	nsv3719	chr3:20133243-20150202	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	esv1828816	chr3:20136508-20389045	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13069629	SGOL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20116400-20194800	Weak transcription	NHDF-Ad	bronchial
2	chr3:20123000-20138400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:20123000-20140800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:20123000-20153000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:20123200-20138600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:20123200-20141000	Weak transcription	Stomach Mucosa	stomach
7	chr3:20123200-20153200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:20128200-20175800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:20131200-20140200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:20131400-20140800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:20131800-20153000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:20132200-20139600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:20132800-20152400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:20134000-20140200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:20134200-20140200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:20134400-20140800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:20134600-20143200	Strong transcription	Primary B cells from peripheral blood	blood
18	chr3:20134600-20145400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:20134800-20140400	Strong transcription	Primary T cells from cord blood	blood
20	chr3:20134800-20143000	Strong transcription	Primary B cells from cord blood	blood
21	chr3:20135200-20145800	Weak transcription	Fetal Brain Female	brain
22	chr3:20135200-20173800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:20135800-20138400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr3:20135800-20138800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:20135800-20140600	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr3:20135800-20141200	Strong transcription	Thymus	Thymus
27	chr3:20136000-20138600	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:20136000-20141200	Weak transcription	Fetal Brain Male	brain
29	chr3:20136200-20138400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:20136200-20140200	Weak transcription	Dnd41	blood
31	chr3:20136200-20145400	Strong transcription	Fetal Thymus	thymus
32	chr3:20136400-20143200	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr3:20136600-20143800	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr3:20136800-20140000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:20136800-20140200	Weak transcription	Brain Germinal Matrix	brain
36	chr3:20136800-20143200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr3:20137000-20139800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
38	chr3:20137000-20150000	Weak transcription	K562	blood
39	chr3:20137200-20138600	Enhancers	Psoas Muscle	Psoas
40	chr3:20137200-20138800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:20137200-20138800	Enhancers	Colon Smooth Muscle	Colon
42	chr3:20137200-20140600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:20137200-20141000	Strong transcription	Fetal Stomach	stomach
44	chr3:20137400-20138800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
45	chr3:20137400-20138800	Enhancers	Ovary	ovary
46	chr3:20137400-20138800	Enhancers	Pancreas	Pancrea
47	chr3:20137400-20139600	Weak transcription	Fetal Lung	lung
48	chr3:20137400-20140800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr3:20137400-20156600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:20137600-20138800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links