Variant report

Variant	rs10775569
Chromosome Location	chr19:56807254-56807255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56806540..56808650-chr19:56825989..56828485,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZSCAN5C-1	chr19:56807143-56807336	NONHSAT068093
2	lnc-ZSCAN5C-1	chr19:56807197-56807336	NONHSAT068095

Variant related genes	Relation type
ENSG00000267549	Chromatin interaction
ENSG00000200646	Chromatin interaction
ENSG00000131848	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10427066	0.89[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12978406	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12978758	0.89[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35063209	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801165	1.00[ASN][1000 genomes]
rs4801307	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801698	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55700397	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249172	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257662	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
4	nsv526325	chr19:56741186-56852035	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
6	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
7	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
8	nsv912517	chr19:56794645-56822466	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
10	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
11	nsv1058026	chr19:56799847-56833153	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10775569	ZNF17	cis	parietal	SCAN
rs10775569	ZSCAN22	cis	cerebellum	SCAN
rs10775569	SOD3	trans	cerebellum	SCAN
rs10775569	ZNF606	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56753000-56809000	Weak transcription	Gastric	stomach
2	chr19:56771400-56817200	Weak transcription	Fetal Brain Male	brain
3	chr19:56772800-56807600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr19:56772800-56824200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr19:56773000-56807400	Weak transcription	Esophagus	oesophagus
6	chr19:56775800-56815600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr19:56779600-56820200	Weak transcription	Hela-S3	cervix
8	chr19:56782800-56825200	Weak transcription	Psoas Muscle	Psoas
9	chr19:56783000-56825000	Weak transcription	Stomach Mucosa	stomach
10	chr19:56785400-56823600	Weak transcription	Osteobl	bone
11	chr19:56786800-56813000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr19:56788200-56824400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr19:56788800-56813000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr19:56789000-56817400	Weak transcription	Small Intestine	intestine
15	chr19:56789000-56823800	Weak transcription	Brain Angular Gyrus	brain
16	chr19:56790600-56820000	Weak transcription	Primary B cells from cord blood	blood
17	chr19:56794000-56813000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:56796400-56816600	Weak transcription	Fetal Kidney	kidney
19	chr19:56796600-56813000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr19:56797600-56811800	Strong transcription	Fetal Stomach	stomach
21	chr19:56798200-56813000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr19:56799800-56825200	Weak transcription	Right Atrium	heart
23	chr19:56800800-56817400	Weak transcription	Fetal Brain Female	brain
24	chr19:56801400-56814800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr19:56801600-56812800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr19:56802200-56810600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr19:56802400-56807800	Strong transcription	Duodenum Mucosa	Duodenum
28	chr19:56802400-56821800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr19:56802600-56809400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:56802800-56813000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr19:56803000-56807800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:56803000-56808200	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr19:56803000-56809400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr19:56803000-56812800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr19:56803000-56813000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr19:56803000-56816600	Weak transcription	Dnd41	blood
37	chr19:56803000-56824200	Weak transcription	Fetal Thymus	thymus
38	chr19:56803200-56807600	Strong transcription	Fetal Lung	lung
39	chr19:56803200-56808000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:56803200-56808000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr19:56803200-56808000	Strong transcription	HepG2	liver
42	chr19:56803200-56808200	Strong transcription	Fetal Intestine Large	intestine
43	chr19:56803200-56809400	Strong transcription	Stomach Smooth Muscle	stomach
44	chr19:56803200-56825000	Weak transcription	Colon Smooth Muscle	Colon
45	chr19:56803600-56808200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr19:56803600-56816600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:56804000-56808200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr19:56804200-56807800	Strong transcription	Fetal Muscle Leg	muscle
49	chr19:56804200-56807800	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr19:56804200-56808000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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