Variant report

Variant	rs2562405
Chromosome Location	chr19:21598623-21598624
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	chr19:21596819..21599115-chr19:21600673..21603133,2	MCF-7	breast:

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10414834	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10424079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666213	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11666447	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11666525	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11666540	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11667103	0.83[EUR][1000 genomes]
rs11667361	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11669033	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11669790	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11670815	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11670868	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11672341	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11672583	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11673320	0.81[AMR][1000 genomes]
rs11879901	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13346641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1621154	0.83[EUR][1000 genomes]
rs1626404	0.83[EUR][1000 genomes]
rs1762578	0.83[EUR][1000 genomes]
rs17680605	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1781867	0.83[EUR][1000 genomes]
rs1781872	0.83[EUR][1000 genomes]
rs1967182	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061916	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2154302	0.81[EUR][1000 genomes]
rs2358993	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2359144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359145	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2562411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562413	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562416	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2650776	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2650844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650848	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3853837	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3853838	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4321312	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4327181	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4359573	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4544364	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4638726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55756795	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55790393	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55875743	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55899865	0.83[EUR][1000 genomes]
rs57299552	0.83[EUR][1000 genomes]
rs58412280	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs60173523	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61035285	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62107465	0.81[EUR][1000 genomes]
rs62107469	0.81[EUR][1000 genomes]
rs62107472	0.83[EUR][1000 genomes]
rs62107479	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62107531	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62107532	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62107534	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62107536	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62107539	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62107540	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62107541	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62109225	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62109226	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62109227	0.86[AMR][1000 genomes]
rs62109228	0.86[AMR][1000 genomes]
rs62109229	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62110367	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62110377	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62110416	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62110420	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62110424	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62110426	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62110427	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62110428	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62110429	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7246339	0.83[EUR][1000 genomes]
rs7251135	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7258099	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7258473	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7258562	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73537884	0.84[AMR][1000 genomes];0.84[EUR][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	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
2	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
3	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
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers 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	35 gene(s)	inside rSNPs	diseases
5	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription 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	15 gene(s)	inside rSNPs	diseases
6	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
7	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers 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 target site	31 gene(s)	inside rSNPs	diseases
8	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	esv1793996	chr19:21544242-21609607	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv1801985	chr19:21544242-21609607	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv1844586	chr19:21544242-21609607	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv1834499	chr19:21557835-21609607	Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv1834993	chr19:21557835-21609607	Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv911421	chr19:21579718-21613397	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
15	nsv578953	chr19:21586797-21609607	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
16	nsv578954	chr19:21587261-21604510	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2562405	RP11-678G14.2	cis	Whole Blood	GTEx
rs2562405	CTD-2561J22.5	cis	Thyroid	GTEx
rs2562405	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21580600-21600200	Weak transcription	Gastric	stomach
2	chr19:21580600-21602400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:21581000-21598800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:21581400-21598800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr19:21581600-21601800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr19:21581800-21607000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:21585000-21614000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:21586000-21599400	Weak transcription	Spleen	Spleen
9	chr19:21590000-21600200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr19:21590200-21606400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
11	chr19:21590600-21608200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
12	chr19:21590800-21601200	Strong transcription	Ovary	ovary
13	chr19:21591600-21599000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr19:21591800-21607000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
15	chr19:21592800-21601200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr19:21593200-21602400	Weak transcription	HSMM	muscle
17	chr19:21593400-21610200	ZNF genes & repeats	Liver	Liver
18	chr19:21593600-21606600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:21593800-21598800	Strong transcription	Adipose Nuclei	Adipose
20	chr19:21594000-21600400	Strong transcription	Left Ventricle	heart
21	chr19:21594200-21601200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
22	chr19:21595000-21598800	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr19:21595000-21599800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr19:21595000-21601400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr19:21595400-21601200	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr19:21595400-21601400	Strong transcription	Fetal Intestine Large	intestine
27	chr19:21595600-21599200	Strong transcription	Brain Germinal Matrix	brain
28	chr19:21596600-21599600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:21596600-21599600	Weak transcription	Fetal Stomach	stomach
30	chr19:21596600-21600200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:21596600-21600800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:21596800-21599600	Weak transcription	Fetal Intestine Small	intestine
33	chr19:21596800-21601200	Weak transcription	Fetal Muscle Leg	muscle
34	chr19:21597000-21598800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr19:21597000-21599600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr19:21597000-21600800	Weak transcription	Pancreas	Pancrea
37	chr19:21597000-21601000	Weak transcription	Placenta	Placenta
38	chr19:21597000-21601200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:21597000-21602200	Weak transcription	HSMMtube	muscle
40	chr19:21597200-21599600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr19:21597200-21599600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr19:21597200-21599600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr19:21597200-21600000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr19:21597200-21600000	Weak transcription	Brain Substantia Nigra	brain
45	chr19:21597200-21600000	Weak transcription	Fetal Lung	lung
46	chr19:21597200-21600400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr19:21597200-21600400	Weak transcription	Lung	lung
48	chr19:21597200-21601200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr19:21597200-21601800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr19:21597200-21602400	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links