Variant report

Variant	rs12609934
Chromosome Location	chr19:18886431-18886432
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18836550..18839278-chr19:18885925..18888717,2	K562	blood:
2	chr19:18884413..18887113-chr19:18941934..18943806,2	MCF-7	breast:
3	chr19:18858094..18859912-chr19:18886098..18888648,2	K562	blood:
4	chr19:18884520..18886788-chr19:18893936..18895702,2	MCF-7	breast:
5	chr19:18848604..18850692-chr19:18885341..18887518,2	K562	blood:
6	chr19:18885317..18890245-chr19:18892616..18897433,6	MCF-7	breast:
7	chr19:18880004..18881941-chr19:18884562..18887049,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000005007	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12611313	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975249	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17757406	0.82[EUR][1000 genomes]
rs1989888	0.88[ASN][1000 genomes]
rs2240014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28494505	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3746266	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3787050	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808155	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56090467	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7257846	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs730079	0.89[ASN][1000 genomes]
rs739638	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv911293	chr19:18872917-19050957	Flanking Active TSS Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv911294	chr19:18872917-19093619	Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv911295	chr19:18874483-18902592	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv911296	chr19:18874483-18915988	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv833777	chr19:18875936-19031076	Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18854600-18895800	Weak transcription	Right Atrium	heart
2	chr19:18862600-18888400	Weak transcription	Aorta	Aorta
3	chr19:18864600-18887400	Weak transcription	Primary B cells from cord blood	blood
4	chr19:18865400-18887400	Weak transcription	Primary T cells from cord blood	blood
5	chr19:18865600-18894600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr19:18865600-18896000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr19:18868200-18890600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:18873800-18889200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr19:18873800-18889200	Weak transcription	Left Ventricle	heart
10	chr19:18873800-18895600	Weak transcription	Ovary	ovary
11	chr19:18873800-18896200	Weak transcription	Brain Angular Gyrus	brain
12	chr19:18874000-18887000	Weak transcription	Colon Smooth Muscle	Colon
13	chr19:18875200-18889200	Weak transcription	Adipose Nuclei	Adipose
14	chr19:18876000-18886800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr19:18876000-18886800	Weak transcription	A549	lung
16	chr19:18876200-18886600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:18876200-18886800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr19:18876200-18888800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:18876400-18886600	Weak transcription	Osteobl	bone
20	chr19:18876400-18887600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr19:18876400-18888600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:18878800-18887200	Strong transcription	Brain Germinal Matrix	brain
23	chr19:18879000-18887600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:18880000-18886600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr19:18880000-18886600	Strong transcription	Fetal Stomach	stomach
26	chr19:18880200-18888000	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr19:18880400-18887000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr19:18880400-18887600	Weak transcription	Colonic Mucosa	Colon
29	chr19:18880600-18886600	Weak transcription	HSMM	muscle
30	chr19:18880600-18886800	Weak transcription	Brain Hippocampus Middle	brain
31	chr19:18880600-18887200	Weak transcription	Brain Substantia Nigra	brain
32	chr19:18880600-18888000	Strong transcription	Fetal Intestine Small	intestine
33	chr19:18880600-18888400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:18880600-18889400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr19:18880600-18895800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr19:18880800-18892600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr19:18881000-18887200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr19:18881800-18886800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr19:18882000-18890600	Weak transcription	Brain Anterior Caudate	brain
40	chr19:18882600-18888000	Weak transcription	Gastric	stomach
41	chr19:18882800-18887400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr19:18883000-18889600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:18883200-18888600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr19:18883400-18889200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr19:18883800-18888000	Weak transcription	Fetal Heart	heart
46	chr19:18884200-18886800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr19:18884200-18886800	Weak transcription	Pancreas	Pancrea
48	chr19:18884200-18886800	Weak transcription	NHEK	skin
49	chr19:18884200-18893000	Weak transcription	Esophagus	oesophagus
50	chr19:18884400-18886600	Weak transcription	HMEC	breast

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