Variant report

Variant	rs2015769
Chromosome Location	chr2:113957637-113957638
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113931492..113932996-chr2:113955583..113957836,2	MCF-7	breast:
2	chr2:113956422..113958569-chr2:113991553..113994219,2	MCF-7	breast:
3	chr2:113949542..113953586-chr2:113955251..113958622,5	MCF-7	breast:
4	chr2:113837298..113838414-chr2:113957612..113958528,4	MCF-7	breast:
5	chr2:113895343..113896160-chr2:113957461..113958420,2	MCF-7	breast:
6	chr2:113956911..113959239-chr2:113960727..113963043,2	MCF-7	breast:
7	chr2:113956459..113959352-chr2:113984317..113985947,2	K562	blood:
8	chr2:113956609..113958908-chr2:113996941..113999634,4	MCF-7	breast:
9	chr2:113955248..113957880-chr2:113994557..113996875,2	MCF-7	breast:
10	chr2:113896084..113896884-chr2:113957485..113958379,3	MCF-7	breast:
11	chr2:113927356..113929479-chr2:113956960..113958587,2	MCF-7	breast:
12	chr2:113933537..113935192-chr2:113956517..113958039,2	MCF-7	breast:
13	chr2:113947298..113949233-chr2:113956219..113958532,2	MCF-7	breast:
14	chr2:113894223..113895276-chr2:113957564..113958721,4	MCF-7	breast:
15	chr2:113912322..113918193-chr2:113953978..113958305,10	MCF-7	breast:
16	chr2:113913769..113918338-chr2:113954843..113958220,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000125637	Chromatin interaction
ENSG00000189223	Chromatin interaction
ENSG00000258395	Chromatin interaction
ENSG00000125618	Chromatin interaction
ENSG00000234174	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12612729	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12619508	0.84[EUR][1000 genomes]
rs12620738	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2019137	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241978	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2276561	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2305133	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3748916	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3811059	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3828188	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3828189	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4848318	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4849169	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4849176	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4849177	0.80[ASN][1000 genomes]
rs4849183	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62160781	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6755639	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs731834	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs895412	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs902695	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs902696	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][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	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv582711	chr2:113895516-113984503	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv582712	chr2:113932431-113985170	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv874899	chr2:113935407-113962071	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv874900	chr2:113948378-113967990	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2015769	AC016683.6	cis	lung	GTEx
rs2015769	PAX8	cis	Esophagus Mucosa	GTEx
rs2015769	PAX8	cis	lung	GTEx
rs2015769	AC016683.6	cis	Esophagus Mucosa	GTEx
rs2015769	AC016683.6	cis	Artery Tibial	GTEx
rs2015769	PAX8	cis	Esophagus Muscularis	GTEx
rs2015769	AC016683.6	cis	Muscle Skeletal	GTEx
rs2015769	AC016683.6	cis	Nerve Tibial	GTEx
rs2015769	AC016683.6	cis	Esophagus Muscularis	GTEx
rs2015769	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs2015769	AC016683.6	cis	Whole Blood	GTEx
rs2015769	PAX8	cis	Adipose Subcutaneous	GTEx
rs2015769	LOC654433	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113940000-113961000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr2:113942800-113961000	Strong transcription	Dnd41	blood
3	chr2:113947400-113961000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr2:113947800-113959600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
5	chr2:113947800-113960600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:113948600-113961000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:113949000-113961200	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr2:113950000-113961000	Strong transcription	Primary T cells from cord blood	blood
9	chr2:113952600-113957800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:113955800-113958000	Weak transcription	K562	blood
11	chr2:113955800-113959200	Enhancers	Stomach Mucosa	stomach
12	chr2:113956000-113957800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:113956000-113958200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:113956800-113957800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:113956800-113959800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:113956800-113961000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:113956800-113962200	Strong transcription	GM12878-XiMat	blood
18	chr2:113957000-113957800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:113957000-113957800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr2:113957000-113957800	Flanking Active TSS	Hela-S3	cervix
21	chr2:113957000-113958000	Weak transcription	Left Ventricle	heart
22	chr2:113957000-113958400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:113957000-113959600	Enhancers	Placenta Amnion	Placenta Amnion
24	chr2:113957000-113960600	Strong transcription	Spleen	Spleen
25	chr2:113957200-113957800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr2:113957200-113957800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:113957200-113957800	Enhancers	Duodenum Mucosa	Duodenum
28	chr2:113957200-113957800	Enhancers	Placenta	Placenta
29	chr2:113957200-113957800	Weak transcription	Gastric	stomach
30	chr2:113957200-113958000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:113957200-113958000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:113957200-113958000	Weak transcription	Colonic Mucosa	Colon
33	chr2:113957200-113958000	Weak transcription	Fetal Lung	lung
34	chr2:113957200-113958200	Enhancers	HSMMtube	muscle
35	chr2:113957200-113958400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:113957200-113958400	Enhancers	NHDF-Ad	bronchial
37	chr2:113957200-113958600	Enhancers	HSMM	muscle
38	chr2:113957200-113958800	Enhancers	NHLF	lung
39	chr2:113957200-113959000	Enhancers	Fetal Heart	heart
40	chr2:113957200-113959600	Weak transcription	Brain Germinal Matrix	brain
41	chr2:113957200-113959600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:113957200-113959600	Weak transcription	Brain Substantia Nigra	brain
43	chr2:113957200-113959800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:113957200-113960000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:113957200-113960000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr2:113957200-113960400	Weak transcription	Osteobl	bone
47	chr2:113957200-113960800	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr2:113957200-113961000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:113957200-113961000	Strong transcription	Primary B cells from cord blood	blood
50	chr2:113957200-113961000	Strong transcription	Primary T cells fromperipheralblood	blood

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