Variant report

Variant	rs12459808
Chromosome Location	chr19:37289780-37289781
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	chr19:37287538..37289947-chr19:37340425..37342708,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251247	Chromatin interaction
ENSG00000197863	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10408063	1.00[ASN][1000 genomes]
rs10410939	1.00[ASN][1000 genomes]
rs10411150	0.90[ASN][1000 genomes]
rs10413876	1.00[ASN][1000 genomes]
rs10414240	1.00[ASN][1000 genomes]
rs10418271	1.00[ASN][1000 genomes]
rs11880022	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880088	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11880159	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11882245	1.00[EUR][1000 genomes]
rs11882652	1.00[EUR][1000 genomes]
rs11882672	1.00[EUR][1000 genomes]
rs11883006	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11883155	1.00[EUR][1000 genomes]
rs11883207	1.00[EUR][1000 genomes]
rs11883279	1.00[EUR][1000 genomes]
rs1227559	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1227561	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459208	1.00[ASN][1000 genomes]
rs12459218	1.00[ASN][1000 genomes]
rs12459243	1.00[ASN][1000 genomes]
rs12459325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459377	0.90[ASN][1000 genomes]
rs12459429	1.00[ASN][1000 genomes]
rs12459527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12459894	0.90[ASN][1000 genomes]
rs12459915	1.00[ASN][1000 genomes]
rs12459923	1.00[ASN][1000 genomes]
rs12460049	1.00[ASN][1000 genomes]
rs12460354	1.00[ASN][1000 genomes]
rs12460418	1.00[ASN][1000 genomes]
rs12460420	1.00[ASN][1000 genomes]
rs12460430	1.00[ASN][1000 genomes]
rs12460455	1.00[ASN][1000 genomes]
rs12460482	1.00[ASN][1000 genomes]
rs12460729	1.00[ASN][1000 genomes]
rs12460774	1.00[ASN][1000 genomes]
rs12461023	1.00[ASN][1000 genomes]
rs12461264	1.00[ASN][1000 genomes]
rs12461265	1.00[ASN][1000 genomes]
rs12461280	1.00[ASN][1000 genomes]
rs12461436	1.00[ASN][1000 genomes]
rs12461474	1.00[ASN][1000 genomes]
rs12461707	1.00[ASN][1000 genomes]
rs12461721	1.00[ASN][1000 genomes]
rs12461723	1.00[ASN][1000 genomes]
rs12461738	1.00[ASN][1000 genomes]
rs12461954	1.00[ASN][1000 genomes]
rs12461970	1.00[ASN][1000 genomes]
rs12462037	1.00[ASN][1000 genomes]
rs12462268	1.00[ASN][1000 genomes]
rs12462281	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462325	1.00[ASN][1000 genomes]
rs12462454	1.00[ASN][1000 genomes]
rs12462471	0.90[ASN][1000 genomes]
rs12462635	1.00[ASN][1000 genomes]
rs12462921	1.00[ASN][1000 genomes]
rs12463012	0.90[ASN][1000 genomes]
rs12974130	1.00[ASN][1000 genomes]
rs12974446	1.00[ASN][1000 genomes]
rs1625762	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1673083	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16971568	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17468285	1.00[ASN][1000 genomes]
rs1990964	0.90[ASN][1000 genomes]
rs2385414	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2385565	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs25419	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs25420	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28398875	1.00[ASN][1000 genomes]
rs28465595	1.00[ASN][1000 genomes]
rs28472526	1.00[ASN][1000 genomes]
rs28645577	1.00[ASN][1000 genomes]
rs28742010	1.00[ASN][1000 genomes]
rs28818888	1.00[ASN][1000 genomes]
rs34051375	1.00[ASN][1000 genomes]
rs34106502	1.00[ASN][1000 genomes]
rs35621405	1.00[ASN][1000 genomes]
rs35706444	1.00[ASN][1000 genomes]
rs3859520	0.90[ASN][1000 genomes]
rs485256	1.00[EUR][1000 genomes]
rs491951	0.90[ASN][1000 genomes]
rs500244	0.90[ASN][1000 genomes]
rs58245911	1.00[ASN][1000 genomes]
rs60268308	1.00[ASN][1000 genomes]
rs60615280	1.00[ASN][1000 genomes]
rs61750934	1.00[ASN][1000 genomes]
rs6510562	1.00[ASN][1000 genomes]
rs73609133	1.00[ASN][1000 genomes]
rs73612031	1.00[ASN][1000 genomes]
rs73612043	1.00[ASN][1000 genomes]
rs73615692	1.00[ASN][1000 genomes]
rs73615693	0.90[ASN][1000 genomes]
rs7508258	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104355	0.90[ASN][1000 genomes]
rs8111419	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	nsv469794	chr19:37129858-37310257	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv482392	chr19:37129858-37310257	ZNF genes & repeats Weak transcription Strong transcription Active TSS 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	27 gene(s)	inside rSNPs	diseases
8	esv34384	chr19:37134068-37330613	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv817833	chr19:37146694-37357289	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription 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 miRNA target site	33 gene(s)	inside rSNPs	diseases
10	esv3517005	chr19:37193712-37364110	Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	esv3517004	chr19:37193762-37363960	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
12	esv3517006	chr19:37193762-37363960	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	nsv911650	chr19:37241141-37331614	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
14	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
15	nsv963042	chr19:37271305-37296858	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
16	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
17	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
18	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
19	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

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37287400-37289800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr19:37287400-37290000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr19:37287400-37327400	ZNF genes & repeats	Liver	Liver
4	chr19:37287600-37289800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr19:37287600-37289800	Active TSS	Duodenum Mucosa	Duodenum
6	chr19:37287600-37289800	Active TSS	NHLF	lung
7	chr19:37287600-37290000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:37287600-37290000	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr19:37287600-37290200	Active TSS	Colon Smooth Muscle	Colon
10	chr19:37287600-37290200	ZNF genes & repeats	Fetal Brain Male	brain
11	chr19:37287600-37290200	ZNF genes & repeats	A549	lung
12	chr19:37287600-37291000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
13	chr19:37287800-37289800	Active TSS	NHDF-Ad	bronchial
14	chr19:37287800-37290200	ZNF genes & repeats	GM12878-XiMat	blood
15	chr19:37287800-37294800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:37288000-37290000	Active TSS	Fetal Heart	heart
17	chr19:37289000-37289800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:37289000-37289800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr19:37289000-37289800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr19:37289000-37289800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:37289000-37290200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr19:37289000-37290200	Weak transcription	Stomach Mucosa	stomach
23	chr19:37289000-37290600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr19:37289000-37290800	Weak transcription	Brain Substantia Nigra	brain
25	chr19:37289000-37292600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr19:37289000-37293600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr19:37289000-37293600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr19:37289000-37295000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
29	chr19:37289000-37296400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr19:37289000-37309200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:37289200-37289800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:37289200-37289800	Enhancers	Primary B cells from cord blood	blood
33	chr19:37289200-37289800	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr19:37289200-37289800	Weak transcription	Brain Hippocampus Middle	brain
35	chr19:37289200-37289800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr19:37289200-37289800	Enhancers	Fetal Stomach	stomach
37	chr19:37289200-37289800	Weak transcription	Ovary	ovary
38	chr19:37289200-37289800	Weak transcription	HSMM	muscle
39	chr19:37289200-37290000	Weak transcription	Fetal Kidney	kidney
40	chr19:37289200-37290200	Weak transcription	Brain Germinal Matrix	brain
41	chr19:37289200-37290200	Weak transcription	NH-A	brain
42	chr19:37289200-37290400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:37289200-37290400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr19:37289200-37290600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
45	chr19:37289200-37290800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr19:37289200-37291600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr19:37289200-37292000	Weak transcription	Osteobl	bone
48	chr19:37289200-37300600	Weak transcription	Right Ventricle	heart
49	chr19:37289200-37301600	Weak transcription	HSMMtube	muscle
50	chr19:37289200-37327000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links