Variant report

Variant	rs12980860
Chromosome Location	chr19:21335239-21335240
allele	G/T
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	POLR2A	chr19:21334434-21335717	K562	blood:	n/a	n/a
2	POLR2A	chr19:21335077-21335244	K562	blood:	n/a	n/a
3	POLR2A	chr19:21335052-21335326	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
RPL7AP10	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10406253	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10407190	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10408496	0.96[ASN][1000 genomes]
rs10414473	0.82[AFR][1000 genomes]
rs10854042	0.96[ASN][1000 genomes]
rs11668640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671623	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12608652	0.81[AFR][1000 genomes]
rs1864208	0.96[ASN][1000 genomes]
rs1975056	0.93[ASN][1000 genomes]
rs2115498	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2358806	0.99[ASN][1000 genomes]
rs2358807	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2884555	0.83[ASN][1000 genomes]
rs29728	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs416001	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4324267	0.93[ASN][1000 genomes]
rs6511202	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6511204	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6511205	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6511206	0.80[ASN][1000 genomes]
rs70950324	0.83[ASN][1000 genomes]
rs7248419	0.87[EUR][1000 genomes]
rs7250691	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7250987	0.96[ASN][1000 genomes]
rs7251158	0.99[ASN][1000 genomes]
rs7251646	0.99[ASN][1000 genomes]
rs7254094	0.81[ASN][1000 genomes]
rs7256576	0.99[ASN][1000 genomes]
rs7258575	0.85[AFR][1000 genomes]
rs8101918	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110848	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv817536	chr19:21041855-21348237	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv960811	chr19:21200306-21371757	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv3399352	chr19:21232738-21423323	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1065384	chr19:21249321-21350698	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv911413	chr19:21263518-21347598	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	esv3319019	chr19:21268262-21336383	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv3319020	chr19:21268262-21336383	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	esv3420290	chr19:21272477-21336432	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	esv7204	chr19:21274198-21336396	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
12	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription 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	41 gene(s)	inside rSNPs	diseases
13	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21325400-21361800	Weak transcription	Small Intestine	intestine
2	chr19:21325600-21365800	Weak transcription	Brain Angular Gyrus	brain
3	chr19:21326000-21337000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:21326000-21338400	Weak transcription	Aorta	Aorta
5	chr19:21326000-21352600	Weak transcription	Right Ventricle	heart
6	chr19:21326000-21361000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:21326200-21336200	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr19:21326200-21336200	Strong transcription	Adipose Nuclei	Adipose
9	chr19:21326200-21336800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr19:21326200-21337000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:21326400-21336200	Strong transcription	Fetal Lung	lung
12	chr19:21326400-21336600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:21326600-21336200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:21326600-21336400	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr19:21326600-21337000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:21326800-21336200	Strong transcription	HSMMtube	muscle
17	chr19:21326800-21336400	Strong transcription	Primary B cells from peripheral blood	blood
18	chr19:21326800-21336400	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr19:21326800-21361800	Weak transcription	Stomach Mucosa	stomach
20	chr19:21327000-21336400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr19:21327000-21336600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr19:21327000-21337000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:21327000-21342800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr19:21327000-21347000	Weak transcription	Hela-S3	cervix
25	chr19:21327400-21336200	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr19:21327400-21336600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr19:21327400-21336800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr19:21327400-21336800	Strong transcription	Duodenum Mucosa	Duodenum
29	chr19:21327600-21337000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:21327800-21336200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr19:21328200-21337000	ZNF genes & repeats	Fetal Brain Female	brain
32	chr19:21328800-21336800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr19:21329200-21336200	Strong transcription	K562	blood
34	chr19:21329400-21336000	ZNF genes & repeats	Brain Germinal Matrix	brain
35	chr19:21329800-21335800	Strong transcription	HSMM	muscle
36	chr19:21330400-21335800	Weak transcription	Fetal Heart	heart
37	chr19:21330400-21336000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr19:21330600-21336200	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr19:21331000-21371000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr19:21331200-21340000	Weak transcription	NHLF	lung
41	chr19:21331400-21336200	Strong transcription	Primary B cells from cord blood	blood
42	chr19:21331600-21335800	ZNF genes & repeats	GM12878-XiMat	blood
43	chr19:21331600-21336600	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr19:21331800-21336200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr19:21331800-21336200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:21331800-21336200	Strong transcription	A549	lung
47	chr19:21332000-21336200	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr19:21332200-21335600	Strong transcription	Fetal Stomach	stomach
49	chr19:21332200-21335800	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr19:21332200-21336000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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