Variant report

Variant	rs12978339
Chromosome Location	chr19:18231381-18231382
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18230201..18232157-chr19:18244427..18246391,2	MCF-7	breast:
2	chr19:18226626..18231621-chr19:18270177..18272430,5	K562	blood:
3	chr19:18230619..18232487-chr19:18234110..18236798,2	K562	blood:
4	chr19:18226689..18233128-chr19:18261137..18272674,17	K562	blood:
5	chr19:18230618..18232554-chr19:18239457..18241659,2	MCF-7	breast:
6	chr19:18226691..18231532-chr19:18258960..18265353,9	MCF-7	breast:
7	chr19:18226427..18233128-chr19:18260600..18269360,14	K562	blood:

Variant related genes	Relation type
ENSG00000269145	Chromatin interaction
ENSG00000268173	Chromatin interaction
ENSG00000099308	Chromatin interaction
ENSG00000105647	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10401175	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10406361	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10409167	0.80[AMR][1000 genomes]
rs11669624	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12981122	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12983325	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12984330	0.80[AMR][1000 genomes]
rs12984449	0.90[EUR][1000 genomes]
rs1566029	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2009030	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2072490	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2270623	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2384858	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3736328	0.84[EUR][1000 genomes]
rs4808116	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71332122	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs740688	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs740691	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8108738	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8112290	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs917551	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055932	chr19:17923918-18369944	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv543923	chr19:17923918-18369944	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats 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	109 gene(s)	inside rSNPs	diseases
3	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
4	nsv470130	chr19:18047283-18234587	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	esv1837595	chr19:18085428-18393682	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
6	nsv833773	chr19:18152971-18302988	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv911241	chr19:18193191-18304700	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv911242	chr19:18201757-18304700	Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv911243	chr19:18206681-18283501	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv911244	chr19:18206681-18304700	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer 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	31 gene(s)	inside rSNPs	diseases
11	nsv911245	chr19:18206681-18338101	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	nsv833774	chr19:18213761-18295329	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv833775	chr19:18213761-18390074	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
14	esv1834142	chr19:18224729-18234588	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
15	nsv911246	chr19:18224729-18283501	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS 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 target site	25 gene(s)	inside rSNPs	diseases
16	nsv911247	chr19:18224729-18288069	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	nsv911248	chr19:18224729-18338101	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
18	nsv911249	chr19:18224729-18375846	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
19	nsv911250	chr19:18224729-18376522	Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
20	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer 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	136 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18229200-18232600	Weak transcription	Aorta	Aorta
2	chr19:18229400-18232200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr19:18229400-18233200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:18229400-18233600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:18229400-18234000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:18229400-18234600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:18229400-18235000	Weak transcription	HSMMtube	muscle
8	chr19:18229400-18243000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr19:18229600-18237000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr19:18229800-18231400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr19:18229800-18231600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:18229800-18232400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:18229800-18233000	Weak transcription	Ovary	ovary
14	chr19:18229800-18233200	Weak transcription	Gastric	stomach
15	chr19:18229800-18233400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr19:18229800-18233400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr19:18229800-18233400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr19:18229800-18239000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:18229800-18239000	Weak transcription	Left Ventricle	heart
20	chr19:18229800-18241400	Weak transcription	HSMM	muscle
21	chr19:18229800-18243000	Weak transcription	Fetal Kidney	kidney
22	chr19:18230000-18231400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:18230000-18231800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr19:18230000-18233400	Weak transcription	Small Intestine	intestine
25	chr19:18230000-18234000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr19:18230000-18235000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:18230000-18239600	Weak transcription	Osteobl	bone
28	chr19:18230000-18241400	Weak transcription	NHDF-Ad	bronchial
29	chr19:18230200-18232000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:18230200-18232200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr19:18230200-18232400	Weak transcription	Lung	lung
32	chr19:18230200-18233000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr19:18230200-18233000	Weak transcription	Fetal Lung	lung
34	chr19:18230200-18233400	Weak transcription	Esophagus	oesophagus
35	chr19:18230200-18233400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr19:18230200-18233600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:18230200-18233600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr19:18230200-18233800	Weak transcription	NHLF	lung
39	chr19:18230200-18235200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:18230200-18239400	Weak transcription	Right Ventricle	heart
41	chr19:18230200-18241200	Weak transcription	Colon Smooth Muscle	Colon
42	chr19:18230200-18246600	Weak transcription	Hela-S3	cervix
43	chr19:18230200-18247200	Weak transcription	NHEK	skin
44	chr19:18230400-18231400	Enhancers	Primary B cells from cord blood	blood
45	chr19:18230400-18231400	Enhancers	Thymus	Thymus
46	chr19:18230400-18232200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr19:18230400-18232200	Weak transcription	Liver	Liver
48	chr19:18230400-18233800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr19:18230400-18236000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr19:18230400-18239400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links