Variant report

Variant	rs73923180
Chromosome Location	chr19:19004622-19004623
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18976234..18978409-chr19:19004531..19006846,2	MCF-7	breast:
2	chr19:18941134..18944715-chr19:19004445..19006890,3	MCF-7	breast:
3	chr19:18993971..18995818-chr19:19002002..19004834,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000005007	Chromatin interaction
ENSG00000223802	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11537890	1.00[AMR][1000 genomes]
rs55639837	1.00[AMR][1000 genomes]
rs55689008	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55982343	1.00[AMR][1000 genomes]
rs56343246	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57534766	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58569954	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv911297	chr19:18928480-19077385	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv911298	chr19:18928480-19093619	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv911300	chr19:18944025-19093619	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
7	nsv470132	chr19:18964442-19054720	Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv911301	chr19:18994638-19077385	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv911302	chr19:18995201-19088981	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18981800-19005800	Weak transcription	Right Atrium	heart
2	chr19:18988000-19005400	Weak transcription	A549	lung
3	chr19:18988200-19004800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr19:18994400-19004800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr19:18994800-19005400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr19:18995000-19004800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr19:18995000-19005200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr19:18995200-19005200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:18997800-19005200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr19:18998200-19004800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:18998200-19005200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr19:18998200-19005400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:18998400-19005200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr19:19002000-19005200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:19004200-19004800	Flanking Active TSS	Brain Substantia Nigra	brain
16	chr19:19004200-19004800	Bivalent Enhancer	Fetal Stomach	stomach
17	chr19:19004200-19004800	Enhancers	HSMM	muscle
18	chr19:19004200-19005000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:19004200-19005000	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr19:19004200-19005200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:19004200-19005200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr19:19004200-19005400	Enhancers	HSMMtube	muscle
23	chr19:19004200-19005800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:19004200-19006200	Enhancers	Fetal Heart	heart
25	chr19:19004400-19004800	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr19:19004400-19004800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:19004400-19004800	Enhancers	Fetal Brain Male	brain
28	chr19:19004400-19005000	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr19:19004400-19005000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
30	chr19:19004400-19005200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:19004400-19005400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:19004400-19005400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
33	chr19:19004400-19005800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
34	chr19:19004400-19005800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
35	chr19:19004400-19006000	Flanking Active TSS	Brain Germinal Matrix	brain
36	chr19:19004600-19004800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr19:19004600-19004800	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr19:19004600-19005000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr19:19004600-19005000	Flanking Active TSS	Brain Angular Gyrus	brain
40	chr19:19004600-19005000	Flanking Active TSS	Fetal Brain Female	brain
41	chr19:19004600-19005000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
42	chr19:19004600-19005200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:19004600-19005200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:19004600-19005200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:19004600-19005800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
46	chr19:19004600-19005800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:19004600-19005800	Bivalent Enhancer	Fetal Lung	lung
48	chr19:19004600-19006200	Bivalent Enhancer	Placenta	Placenta
49	chr19:19004600-19006200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
50	chr19:19004600-19006600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links