Variant report

Variant	rs17562787
Chromosome Location	chr19:45607139-45607140
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:45570554..45573388-chr19:45606765..45608658,2	MCF-7	breast:
2	chr19:45606192..45609291-chr19:45618096..45620954,3	K562	blood:
3	chr19:45580658..45583147-chr19:45605476..45608233,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104859	Chromatin interaction
ENSG00000142252	Chromatin interaction
ENSG00000007047	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10402479	1.00[ASN][1000 genomes]
rs10403214	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405306	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405719	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405721	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10406911	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs10407374	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10408366	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10408462	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs10409138	0.92[CEU][hapmap];1.00[CHD][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409232	0.91[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409727	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409903	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410424	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412988	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10415674	1.00[ASN][1000 genomes]
rs10417101	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417347	1.00[ASN][1000 genomes]
rs10417618	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417804	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10419874	1.00[ASN][1000 genomes]
rs10420717	1.00[ASN][1000 genomes]
rs10420824	1.00[ASN][1000 genomes]
rs10421085	1.00[ASN][1000 genomes]
rs10421425	1.00[ASN][1000 genomes]
rs10421932	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs10422671	1.00[ASN][1000 genomes]
rs10423079	1.00[ASN][1000 genomes]
rs10423555	1.00[ASN][1000 genomes]
rs10424651	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10425380	1.00[ASN][1000 genomes]
rs1076384	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11881409	1.00[CHD][hapmap]
rs12459074	0.80[CEU][hapmap]
rs12459386	1.00[ASN][1000 genomes]
rs12459402	1.00[ASN][1000 genomes]
rs12459945	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461416	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12461749	1.00[ASN][1000 genomes]
rs13344055	1.00[ASN][1000 genomes]
rs13344075	1.00[ASN][1000 genomes]
rs13345307	1.00[ASN][1000 genomes]
rs1541926	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16979688	1.00[ASN][1000 genomes]
rs17562676	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17642665	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982077	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003183	1.00[ASN][1000 genomes]
rs2003345	1.00[ASN][1000 genomes]
rs2004356	1.00[ASN][1000 genomes]
rs2011438	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041261	1.00[ASN][1000 genomes]
rs2041263	1.00[ASN][1000 genomes]
rs2043320	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs2060252	1.00[ASN][1000 genomes]
rs2060253	1.00[ASN][1000 genomes]
rs28404390	1.00[ASN][1000 genomes]
rs28657408	1.00[ASN][1000 genomes]
rs28706378	1.00[ASN][1000 genomes]
rs28719739	1.00[ASN][1000 genomes]
rs35904300	1.00[ASN][1000 genomes]
rs4427916	1.00[ASN][1000 genomes]
rs4608431	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803798	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58260098	1.00[ASN][1000 genomes]
rs58600209	1.00[ASN][1000 genomes]
rs58854055	1.00[ASN][1000 genomes]
rs58880456	1.00[ASN][1000 genomes]
rs59240271	1.00[ASN][1000 genomes]
rs60372869	1.00[ASN][1000 genomes]
rs60455813	1.00[ASN][1000 genomes]
rs61531804	1.00[ASN][1000 genomes]
rs7251651	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7254138	1.00[ASN][1000 genomes]
rs7257566	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7257599	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259404	1.00[ASN][1000 genomes]
rs733289	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73562250	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73562267	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73562286	1.00[ASN][1000 genomes]
rs73939607	1.00[ASN][1000 genomes]
rs747646	1.00[ASN][1000 genomes]
rs747647	1.00[ASN][1000 genomes]
rs754364	1.00[ASN][1000 genomes]
rs754365	1.00[ASN][1000 genomes]
rs754367	1.00[ASN][1000 genomes]
rs8101046	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs892133	1.00[ASN][1000 genomes]
rs9653111	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3449420	chr19:45523560-45626884	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv833842	chr19:45593888-45684308	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17562787	NANOS2	cis	cerebellum	SCAN
rs17562787	EIF5AP3	cis	lung	GTEx
rs17562787	Hs.466924	cis	multi-tissue	Pritchard
rs17562787	DKKL1	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45597400-45609400	Enhancers	Stomach Mucosa	stomach
2	chr19:45597600-45609200	Enhancers	Pancreas	Pancrea
3	chr19:45600000-45607800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:45600800-45607800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:45601400-45608000	Enhancers	Esophagus	oesophagus
6	chr19:45601400-45608000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr19:45602000-45612200	Weak transcription	Hela-S3	cervix
8	chr19:45602400-45607200	Enhancers	NHLF	lung
9	chr19:45602400-45607600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr19:45602800-45612600	Weak transcription	A549	lung
11	chr19:45603400-45609200	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr19:45603600-45607600	Enhancers	Duodenum Mucosa	Duodenum
13	chr19:45603600-45609200	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr19:45603600-45612600	Weak transcription	Dnd41	blood
15	chr19:45603800-45608400	Enhancers	Small Intestine	intestine
16	chr19:45603800-45619600	Weak transcription	HSMMtube	muscle
17	chr19:45604000-45608000	Enhancers	Fetal Muscle Trunk	muscle
18	chr19:45604000-45609600	Enhancers	Fetal Muscle Leg	muscle
19	chr19:45604200-45607400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr19:45604200-45609200	Enhancers	Spleen	Spleen
21	chr19:45604200-45611200	Weak transcription	K562	blood
22	chr19:45604400-45608000	Enhancers	Fetal Kidney	kidney
23	chr19:45604600-45607400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr19:45604600-45609200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr19:45605000-45608000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr19:45605000-45608800	Enhancers	Left Ventricle	heart
27	chr19:45605200-45608000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:45605200-45608800	Enhancers	Lung	lung
29	chr19:45605200-45609200	Enhancers	Gastric	stomach
30	chr19:45605200-45609400	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr19:45605400-45608000	Enhancers	Brain Germinal Matrix	brain
32	chr19:45605600-45608000	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr19:45605600-45608800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:45605800-45607200	Enhancers	Brain Cingulate Gyrus	brain
35	chr19:45605800-45607400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr19:45605800-45607800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr19:45605800-45608600	Enhancers	Fetal Brain Female	brain
38	chr19:45605800-45608600	Enhancers	HMEC	breast
39	chr19:45605800-45608800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr19:45605800-45608800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr19:45605800-45608800	Enhancers	Liver	Liver
42	chr19:45605800-45609000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr19:45605800-45609400	Enhancers	Brain Hippocampus Middle	brain
44	chr19:45605800-45609400	Enhancers	Placenta	Placenta
45	chr19:45605800-45610000	Enhancers	Right Ventricle	heart
46	chr19:45606000-45607400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr19:45606000-45607600	Enhancers	Adipose Nuclei	Adipose
48	chr19:45606000-45607600	Enhancers	Fetal Brain Male	brain
49	chr19:45606000-45607800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:45606000-45607800	Enhancers	Fetal Heart	heart

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