Variant report

Variant	rs274178
Chromosome Location	chr19:56659742-56659743
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:56651213..56654930-chr19:56659725..56661887,5	K562	blood:
2	chr19:56630500..56632010-chr19:56658354..56660515,2	MCF-7	breast:
3	chr19:56651992..56654360-chr19:56657934..56660708,2	MCF-7	breast:
4	chr19:56657919..56660235-chr19:56667044..56669703,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167685	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2637084	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2637085	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs274142	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs274147	0.83[ASN][1000 genomes]
rs274148	0.86[ASN][1000 genomes]
rs274149	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs274150	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs274153	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs274176	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs274179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs274184	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs274185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs502722	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs679557	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7255998	0.92[GIH][hapmap]

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	nsv1056598	chr19:56331762-56703428	Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv580354	chr19:56505685-56723492	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
5	nsv523651	chr19:56537528-56707048	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	nsv1057820	chr19:56555942-56720262	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
7	nsv528998	chr19:56578238-56707048	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv517365	chr19:56592286-56674548	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	nsv912513	chr19:56592286-56685463	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
10	nsv521744	chr19:56592286-56686953	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
11	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
12	nsv528361	chr19:56638845-56688570	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs274178	ZNF549	cis	cerebellum	SCAN
rs274178	ZNF497	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56653400-56661200	Weak transcription	Psoas Muscle	Psoas
2	chr19:56653800-56660200	Weak transcription	Primary B cells from cord blood	blood
3	chr19:56653800-56660400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr19:56653800-56661200	Weak transcription	HSMMtube	muscle
5	chr19:56653800-56664200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:56653800-56664200	Weak transcription	HUVEC	blood vessel
7	chr19:56653800-56667200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:56653800-56669200	Weak transcription	HSMM	muscle
9	chr19:56653800-56669400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr19:56653800-56673000	Weak transcription	Hela-S3	cervix
11	chr19:56653800-56674000	Weak transcription	Fetal Kidney	kidney
12	chr19:56654000-56661000	Weak transcription	Fetal Brain Male	brain
13	chr19:56654000-56662000	Strong transcription	Fetal Stomach	stomach
14	chr19:56654000-56681600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:56654200-56663200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr19:56654200-56674000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr19:56654400-56668400	Weak transcription	HMEC	breast
18	chr19:56654400-56671200	Weak transcription	Small Intestine	intestine
19	chr19:56655200-56661600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr19:56655200-56672200	Weak transcription	NHDF-Ad	bronchial
21	chr19:56655800-56661200	Weak transcription	Osteobl	bone
22	chr19:56656400-56664800	Weak transcription	K562	blood
23	chr19:56656400-56667400	Weak transcription	Stomach Mucosa	stomach
24	chr19:56656400-56672200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr19:56656600-56662000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr19:56656600-56662000	Strong transcription	Dnd41	blood
27	chr19:56656800-56661600	Strong transcription	Fetal Brain Female	brain
28	chr19:56656800-56661800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:56657000-56659800	Genic enhancers	Fetal Muscle Trunk	muscle
30	chr19:56657000-56660400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr19:56657000-56660400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr19:56657000-56660600	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr19:56657000-56661600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr19:56657000-56661600	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr19:56657000-56661800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr19:56657000-56662000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr19:56657000-56662000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:56657000-56662000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:56657000-56662000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr19:56657000-56662000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr19:56657000-56662000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr19:56657000-56662000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr19:56657000-56662000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr19:56657000-56662000	Strong transcription	Fetal Lung	lung
45	chr19:56657200-56660400	Strong transcription	Spleen	Spleen
46	chr19:56657200-56661400	Strong transcription	Stomach Smooth Muscle	stomach
47	chr19:56657200-56661800	Strong transcription	Brain Germinal Matrix	brain
48	chr19:56657200-56662000	Strong transcription	Fetal Thymus	thymus
49	chr19:56657200-56664000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr19:56657400-56660200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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