Variant report

Variant	rs28683678
Chromosome Location	chr19:53757281-53757282
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53756061..53758221-chr19:53835400..53837964,2	K562	blood:
2	chr19:53757171..53759413-chr19:53761510..53763569,2	K562	blood:

Variant related genes	Relation type
ENSG00000196131	Chromatin interaction
ENSG00000213799	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10403807	0.86[EUR][1000 genomes]
rs10404561	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10407257	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10412650	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10419020	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10419211	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10419777	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10424137	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28434722	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28658052	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28676766	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4411615	0.87[EUR][1000 genomes]
rs45575234	0.88[EUR][1000 genomes]
rs56121768	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61576844	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6509740	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7245436	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7246435	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7250202	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7260260	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7260595	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8100275	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8100627	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8107040	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8107688	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8107870	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065143	chr19:53507142-53853363	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv544063	chr19:53507142-53853363	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1058019	chr19:53507142-53904508	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv544064	chr19:53507142-53904508	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv912342	chr19:53581151-54010759	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1063630	chr19:53591444-54419183	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	282 gene(s)	inside rSNPs	diseases
7	nsv1055378	chr19:53603268-53951855	Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv544065	chr19:53603268-53951855	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	esv2830362	chr19:53681132-53933147	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv1055236	chr19:53739483-53778339	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1059899	chr19:53744560-53768337	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1064070	chr19:53744560-53769702	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28683678	ZNF677	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53737400-53757600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:53740200-53757600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:53748400-53757400	Weak transcription	Colonic Mucosa	Colon
4	chr19:53750400-53759200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
5	chr19:53750600-53757600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:53751200-53757400	ZNF genes & repeats	Primary B cells from cord blood	blood
7	chr19:53752400-53759400	ZNF genes & repeats	Liver	Liver
8	chr19:53752600-53757400	Weak transcription	Stomach Mucosa	stomach
9	chr19:53753600-53757400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
10	chr19:53753600-53759000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
11	chr19:53753800-53757600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:53754000-53757400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr19:53754000-53757600	Weak transcription	Esophagus	oesophagus
14	chr19:53754600-53757600	Weak transcription	Gastric	stomach
15	chr19:53754800-53757400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr19:53755000-53757400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:53755200-53757400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr19:53755400-53757400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr19:53755400-53757600	Weak transcription	Pancreas	Pancrea
20	chr19:53755600-53757400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:53755800-53757400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr19:53755800-53757400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr19:53755800-53757400	Weak transcription	HSMM	muscle
24	chr19:53755800-53757600	Weak transcription	Lung	lung
25	chr19:53756000-53757400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr19:53756000-53757400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr19:53756200-53757400	Weak transcription	Aorta	Aorta
28	chr19:53756200-53757400	Weak transcription	Fetal Stomach	stomach
29	chr19:53756200-53757600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:53756600-53757400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr19:53756600-53757400	Weak transcription	Fetal Muscle Leg	muscle
32	chr19:53756600-53757400	Weak transcription	Placenta	Placenta
33	chr19:53756800-53757400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr19:53756800-53757400	Weak transcription	Left Ventricle	heart
35	chr19:53756800-53757400	Weak transcription	Ovary	ovary
36	chr19:53757000-53757400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr19:53757000-53757400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
38	chr19:53757000-53757400	Enhancers	Fetal Heart	heart
39	chr19:53757000-53757400	Weak transcription	Fetal Intestine Large	intestine
40	chr19:53757000-53757400	Flanking Active TSS	Fetal Lung	lung
41	chr19:53757000-53757400	Weak transcription	Fetal Thymus	thymus
42	chr19:53757000-53757400	Flanking Active TSS	Dnd41	blood
43	chr19:53757000-53757600	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr19:53757000-53758000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr19:53757000-53758400	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr19:53757000-53758800	Active TSS	Fetal Kidney	kidney
47	chr19:53757000-53759000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr19:53757000-53759000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr19:53757000-53759200	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr19:53757000-53759200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell

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