Variant report

Variant	rs61995780
Chromosome Location	chr14:104120612-104120613
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:104094508..104097348-chr14:104119011..104121008,3	MCF-7	breast:
2	chr14:104120505..104122040-chr14:104123053..104125123,2	K562	blood:
3	chr14:104091249..104097746-chr14:104118497..104125842,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000126214	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10134399	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10135248	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10143623	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10145755	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10147049	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11624505	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11849259	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2403205	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3783404	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915733	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55864158	0.81[AFR][1000 genomes]
rs55885592	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56660916	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57218990	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58133129	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59217746	0.94[ASN][1000 genomes]
rs6593	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs68087451	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs709400	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7150141	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7359090	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8003090	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8005885	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8018979	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs861531	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs861534	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs861536	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs861538	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs861539	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs861548	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][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	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
2	nsv832883	chr14:103927687-104120953	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv902300	chr14:103967504-104205811	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1052010	chr14:104061472-104216267	Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv542201	chr14:104061472-104216267	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv456435	chr14:104061646-104198251	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
7	nsv566023	chr14:104061646-104198251	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
8	nsv902308	chr14:104087209-104211180	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
9	nsv1041329	chr14:104097750-104196346	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv542202	chr14:104097750-104196346	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv1048866	chr14:104100862-104195896	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
12	nsv542203	chr14:104113463-104143782	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs61995780	APOPT1	cis	Muscle Skeletal	GTEx
rs61995780	BAG5	Cis_1M	lymphoblastoid	RTeQTL
rs61995780	BAG5	cis	multi-tissue	Pritchard
rs61995780	MARK3	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104097400-104120800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr14:104097400-104156600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr14:104101800-104120800	Weak transcription	Hela-S3	cervix
4	chr14:104104800-104120800	Weak transcription	HepG2	liver
5	chr14:104105200-104121800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr14:104105200-104122200	Weak transcription	Fetal Kidney	kidney
7	chr14:104108000-104120800	Weak transcription	HMEC	breast
8	chr14:104108000-104130000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr14:104110000-104122200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr14:104110800-104130000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr14:104113200-104120800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr14:104117600-104120800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr14:104117600-104121800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr14:104117800-104120800	Enhancers	Brain Cingulate Gyrus	brain
15	chr14:104117800-104120800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr14:104117800-104121200	Enhancers	Brain Substantia Nigra	brain
17	chr14:104117800-104122000	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr14:104117800-104129800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr14:104117800-104157000	Strong transcription	Dnd41	blood
20	chr14:104117800-104176000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr14:104118000-104121200	Enhancers	Brain Hippocampus Middle	brain
22	chr14:104118000-104121200	Enhancers	Colon Smooth Muscle	Colon
23	chr14:104118000-104122200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr14:104118400-104120800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr14:104118400-104120800	Genic enhancers	Muscle Satellite Cultured Cells	--
26	chr14:104118400-104120800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr14:104118400-104121000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr14:104118400-104121000	Weak transcription	Psoas Muscle	Psoas
29	chr14:104118400-104121200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr14:104118400-104124600	Strong transcription	Primary B cells from cord blood	blood
31	chr14:104118600-104120800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr14:104118600-104124800	Strong transcription	A549	lung
33	chr14:104118800-104121200	Weak transcription	Gastric	stomach
34	chr14:104118800-104175600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr14:104119000-104132200	Strong transcription	Primary T cells from cord blood	blood
36	chr14:104119200-104121600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr14:104119200-104123800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr14:104119200-104131000	Strong transcription	NHEK	skin
39	chr14:104119200-104145400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr14:104119200-104155600	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr14:104119200-104173000	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr14:104119400-104121200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr14:104119400-104130600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr14:104119400-104145000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr14:104119400-104147800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr14:104119400-104157000	Strong transcription	Fetal Thymus	thymus
47	chr14:104119400-104161800	Strong transcription	Fetal Intestine Small	intestine
48	chr14:104119400-104164600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr14:104119400-104175200	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr14:104119600-104124400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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