Variant report

Variant	rs12461466
Chromosome Location	chr19:39293295-39293296
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39289399..39293459-chr19:39320493..39322736,5	MCF-7	breast:
2	chr19:39292786..39294819-chr19:39320796..39322447,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104823	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12461850	0.83[ASN][1000 genomes]
rs12974874	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12980032	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12980315	0.94[ASN][1000 genomes]
rs12981495	0.83[ASN][1000 genomes]
rs12981542	0.83[ASN][1000 genomes]
rs34465996	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34619818	1.00[ASN][1000 genomes]
rs34960839	0.94[ASN][1000 genomes]
rs58866020	0.94[ASN][1000 genomes]
rs62119011	1.00[ASN][1000 genomes]
rs62121412	0.85[ASN][1000 genomes]
rs71356824	0.81[ASN][1000 genomes]
rs8110828	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1061904	chr19:39249692-39302843	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	nsv911670	chr19:39250308-39322087	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv911671	chr19:39252238-39306425	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
6	nsv911672	chr19:39252238-39318006	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1058132	chr19:39279522-39302843	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39283200-39305600	Weak transcription	Brain Angular Gyrus	brain
2	chr19:39283200-39305600	Weak transcription	Brain Substantia Nigra	brain
3	chr19:39283400-39294000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr19:39283400-39294000	Weak transcription	Pancreas	Pancrea
5	chr19:39283600-39294000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:39283600-39296000	Weak transcription	Left Ventricle	heart
7	chr19:39283600-39296000	Weak transcription	Lung	lung
8	chr19:39283600-39296000	Weak transcription	Right Atrium	heart
9	chr19:39283600-39305600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:39283600-39305800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr19:39283600-39305800	Weak transcription	Brain Hippocampus Middle	brain
12	chr19:39283600-39305800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr19:39283800-39295800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr19:39283800-39295800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr19:39283800-39296000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr19:39283800-39306000	Weak transcription	Primary B cells from cord blood	blood
17	chr19:39284000-39295800	Weak transcription	Primary B cells from peripheral blood	blood
18	chr19:39284000-39305600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:39284000-39318200	Weak transcription	Fetal Kidney	kidney
20	chr19:39284200-39294000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr19:39284200-39305800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr19:39285200-39309400	Weak transcription	Fetal Heart	heart
23	chr19:39289600-39296000	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr19:39289600-39296000	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr19:39289800-39295800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr19:39290000-39296000	Weak transcription	Esophagus	oesophagus
27	chr19:39290200-39296000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:39290200-39296000	Strong transcription	Fetal Intestine Small	intestine
29	chr19:39290200-39305800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr19:39290600-39297600	Weak transcription	A549	lung
31	chr19:39290800-39295800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:39290800-39296000	Weak transcription	NHEK	skin
33	chr19:39290800-39310600	Weak transcription	HMEC	breast
34	chr19:39291000-39296000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr19:39291200-39294800	Strong transcription	Fetal Intestine Large	intestine
36	chr19:39291200-39296000	Weak transcription	Ovary	ovary
37	chr19:39291200-39307400	Weak transcription	Fetal Lung	lung
38	chr19:39291400-39294800	Strong transcription	Liver	Liver
39	chr19:39291400-39295000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr19:39291400-39296000	Strong transcription	Duodenum Mucosa	Duodenum
41	chr19:39291400-39305600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr19:39291600-39295000	Strong transcription	Adipose Nuclei	Adipose
43	chr19:39291600-39295800	Strong transcription	Stomach Mucosa	stomach
44	chr19:39291800-39294800	Strong transcription	Gastric	stomach
45	chr19:39292000-39305800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr19:39292200-39296000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr19:39292400-39294200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr19:39292400-39300400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr19:39292600-39296400	Strong transcription	Colonic Mucosa	Colon
50	chr19:39292600-39301800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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