Variant report

Variant	rs10409206
Chromosome Location	chr19:37412161-37412162
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37405380..37408333-chr19:37412047..37415045,3	MCF-7	breast:
2	chr19:37411760..37413673-chr19:37428843..37431824,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198453	Chromatin interaction
ENSG00000185869	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10401212	0.87[EUR][1000 genomes]
rs10401417	0.86[ASN][1000 genomes]
rs10404981	0.95[ASN][1000 genomes]
rs10405238	0.83[ASN][1000 genomes]
rs10407557	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10407712	0.86[ASN][1000 genomes]
rs10408534	0.82[ASN][1000 genomes]
rs10408951	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10410594	0.85[ASN][1000 genomes]
rs10411251	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10412863	0.86[ASN][1000 genomes]
rs10414781	0.86[ASN][1000 genomes]
rs10414907	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10416960	0.88[ASN][1000 genomes]
rs10418144	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10420859	0.86[ASN][1000 genomes]
rs10424100	0.83[ASN][1000 genomes]
rs11084868	0.88[ASN][1000 genomes]
rs12710052	0.86[ASN][1000 genomes]
rs12977971	0.86[ASN][1000 genomes]
rs12981965	0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs13345230	0.84[ASN][1000 genomes]
rs13345489	0.86[ASN][1000 genomes]
rs1551025	0.86[ASN][1000 genomes]
rs1623097	0.86[ASN][1000 genomes]
rs1624293	0.86[ASN][1000 genomes]
rs1644664	0.85[ASN][1000 genomes]
rs1644701	0.82[ASN][1000 genomes]
rs1667357	0.83[ASN][1000 genomes]
rs1667359	0.83[ASN][1000 genomes]
rs16971771	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16971772	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16971850	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17639910	0.86[ASN][1000 genomes]
rs17707101	0.86[ASN][1000 genomes]
rs2010342	0.88[ASN][1000 genomes]
rs2385470	0.87[EUR][1000 genomes]
rs2595552	0.83[ASN][1000 genomes]
rs28495495	0.88[ASN][1000 genomes]
rs28542490	0.86[ASN][1000 genomes]
rs28555503	0.86[ASN][1000 genomes]
rs28608841	0.86[ASN][1000 genomes]
rs28626335	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28655720	0.86[ASN][1000 genomes]
rs34791663	0.86[ASN][1000 genomes]
rs35881914	0.86[ASN][1000 genomes]
rs3816390	0.86[ASN][1000 genomes]
rs3816391	0.86[ASN][1000 genomes]
rs3955478	0.87[EUR][1000 genomes]
rs4006391	0.88[ASN][1000 genomes]
rs4006392	0.88[ASN][1000 genomes]
rs4805189	0.87[ASN][1000 genomes]
rs4805190	0.88[ASN][1000 genomes]
rs4806376	0.94[ASN][1000 genomes]
rs4806377	0.98[ASN][1000 genomes]
rs4806386	0.85[ASN][1000 genomes]
rs56387564	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60293110	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62113193	0.86[ASN][1000 genomes]
rs62115573	0.88[ASN][1000 genomes]
rs62115574	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62115612	0.94[ASN][1000 genomes]
rs62115615	0.94[ASN][1000 genomes]
rs6510572	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs71266562	0.83[ASN][1000 genomes]
rs71356024	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7249013	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7250498	0.83[ASN][1000 genomes]
rs7251087	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7252797	0.83[ASN][1000 genomes]
rs7257045	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7257251	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7257484	0.86[ASN][1000 genomes]
rs73626774	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8101062	0.81[AFR][1000 genomes]
rs8101922	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9304878	0.88[ASN][1000 genomes]
rs997516	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised 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	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic 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	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic 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	73 gene(s)	inside rSNPs	diseases
6	nsv521605	chr19:37261810-37483444	ZNF genes & repeats Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv1060155	chr19:37274915-37458788	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv544000	chr19:37274915-37458788	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers 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	27 gene(s)	inside rSNPs	diseases
11	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers 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	25 gene(s)	inside rSNPs	diseases
13	nsv911651	chr19:37300554-37428465	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
15	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
16	nsv458569	chr19:37331614-37412887	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv579462	chr19:37331614-37412887	Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
18	nsv523848	chr19:37357289-37487632	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37408200-37413000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr19:37408200-37413000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr19:37408200-37413000	Weak transcription	Aorta	Aorta
4	chr19:37408200-37413000	Weak transcription	Colonic Mucosa	Colon
5	chr19:37408200-37436400	Weak transcription	Fetal Thymus	thymus
6	chr19:37408200-37440600	Weak transcription	Stomach Mucosa	stomach
7	chr19:37408400-37412800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr19:37408400-37412800	Weak transcription	HUVEC	blood vessel
9	chr19:37408400-37413000	Weak transcription	Fetal Intestine Large	intestine
10	chr19:37408400-37413000	Weak transcription	Spleen	Spleen
11	chr19:37408400-37417000	Weak transcription	Fetal Kidney	kidney
12	chr19:37408400-37440600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:37408600-37412600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr19:37408600-37412800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr19:37408600-37412800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr19:37408600-37439600	Weak transcription	Fetal Heart	heart
17	chr19:37408800-37414800	Strong transcription	Fetal Muscle Trunk	muscle
18	chr19:37408800-37415200	Strong transcription	Left Ventricle	heart
19	chr19:37409000-37412800	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr19:37409000-37413800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:37409000-37413800	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr19:37409000-37413800	Strong transcription	Fetal Muscle Leg	muscle
23	chr19:37409000-37414200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr19:37409000-37414800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr19:37409000-37415000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:37409000-37444800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:37409000-37447400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr19:37409200-37412600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr19:37409200-37412800	Strong transcription	Adipose Nuclei	Adipose
30	chr19:37409200-37413000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr19:37409200-37413800	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr19:37409200-37413800	Strong transcription	Brain Anterior Caudate	brain
33	chr19:37409200-37414200	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr19:37409200-37414400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr19:37409200-37414600	Strong transcription	Fetal Lung	lung
36	chr19:37409200-37415000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr19:37409400-37413800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:37409400-37414000	Strong transcription	Fetal Brain Female	brain
39	chr19:37409400-37414800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
40	chr19:37409400-37415000	Strong transcription	Stomach Smooth Muscle	stomach
41	chr19:37409600-37423600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr19:37409800-37413800	Strong transcription	Dnd41	blood
43	chr19:37409800-37416000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr19:37409800-37421400	Weak transcription	Fetal Brain Male	brain
45	chr19:37410000-37413000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr19:37410000-37415400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr19:37410200-37412600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:37410200-37412800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:37410200-37413800	Strong transcription	Fetal Stomach	stomach
50	chr19:37410200-37415000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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