Variant report

Variant	rs12104325
Chromosome Location	chr19:18490284-18490285
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIX5	chr19:18490255-18491454	A549	lung:	n/a	n/a
2	CEBPB	chr19:18490231-18490293	K562	blood:	n/a	n/a
3	ZNF384	chr19:18490155-18490484	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:18482254..18486316-chr19:18487769..18490915,4	MCF-7	breast:
2	chr19:18474398..18477228-chr19:18489482..18491210,2	MCF-7	breast:
3	chr19:18487658..18490624-chr19:18548035..18550250,2	MCF-7	breast:

Variant related genes	Relation type
GDF15	TF binding region
ENSG00000130513	Chromatin interaction
ENSG00000105655	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10424912	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1059369	0.91[ASN][1000 genomes]
rs12460909	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12461382	0.89[ASN][1000 genomes]
rs1804826	0.88[ASN][1000 genomes]
rs2161106	0.83[ASN][1000 genomes]
rs4808790	0.88[ASN][1000 genomes]
rs4808791	0.97[ASN][1000 genomes]
rs4808795	0.89[ASN][1000 genomes]
rs7226	0.82[ASN][1000 genomes]
rs73011458	0.85[ASN][1000 genomes]
rs8105429	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
3	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	162 gene(s)	inside rSNPs	diseases
4	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	nsv428018	chr19:18454891-18663981	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
8	nsv911275	chr19:18484922-18586759	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18483600-18491000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr19:18485200-18490800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:18485200-18491200	Weak transcription	Psoas Muscle	Psoas
4	chr19:18485600-18490800	Weak transcription	Right Atrium	heart
5	chr19:18485800-18490800	Weak transcription	Adipose Nuclei	Adipose
6	chr19:18485800-18490800	Weak transcription	NH-A	brain
7	chr19:18485800-18490800	Weak transcription	NHDF-Ad	bronchial
8	chr19:18485800-18491000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr19:18485800-18491000	Enhancers	HepG2	liver
10	chr19:18485800-18491200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr19:18485800-18491200	Weak transcription	Fetal Heart	heart
12	chr19:18485800-18496600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr19:18485800-18499000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:18486000-18490800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:18486000-18490800	Weak transcription	Colon Smooth Muscle	Colon
16	chr19:18486000-18490800	Weak transcription	Fetal Muscle Leg	muscle
17	chr19:18486000-18490800	Weak transcription	Fetal Thymus	thymus
18	chr19:18486000-18490800	Weak transcription	Stomach Mucosa	stomach
19	chr19:18486000-18490800	Enhancers	Hela-S3	cervix
20	chr19:18486000-18491000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr19:18486000-18491000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr19:18486000-18491000	Weak transcription	Brain Substantia Nigra	brain
23	chr19:18486000-18491200	Weak transcription	Left Ventricle	heart
24	chr19:18486200-18490800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:18486200-18490800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr19:18486200-18491000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:18486200-18491200	Weak transcription	Lung	lung
28	chr19:18486400-18490800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr19:18486400-18496600	Weak transcription	Fetal Kidney	kidney
30	chr19:18486600-18490800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr19:18486600-18491000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr19:18486600-18491000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr19:18487000-18490800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr19:18487400-18492000	Enhancers	Liver	Liver
35	chr19:18487800-18491400	Enhancers	A549	lung
36	chr19:18488000-18490400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr19:18488000-18490800	Enhancers	K562	blood
38	chr19:18488200-18490800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr19:18488600-18492200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:18488600-18496800	Enhancers	Placenta	Placenta
41	chr19:18488800-18490800	Weak transcription	Aorta	Aorta
42	chr19:18488800-18490800	Weak transcription	Fetal Intestine Large	intestine
43	chr19:18488800-18490800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr19:18489000-18490800	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr19:18489000-18491200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr19:18489000-18491800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr19:18489200-18491000	Weak transcription	Right Ventricle	heart
48	chr19:18489400-18490600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:18489400-18492000	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr19:18489600-18490800	Weak transcription	Fetal Intestine Small	intestine

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