Variant report

Variant	rs274182
Chromosome Location	chr19:56656316-56656317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:56655759-56656708	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56615193..56619302-chr19:56653183..56656350,4	MCF-7	breast:
2	chr19:56629015..56635457-chr19:56649954..56657591,25	MCF-7	breast:
3	chr19:56629593..56635165-chr19:56650391..56656450,20	K562	blood:
4	chr19:56627257..56634581-chr19:56650310..56656612,28	MCF-7	breast:
5	chr19:56654924..56657200-chr19:56664145..56666028,2	K562	blood:

No data

Variant related genes	Relation type
ZNF444	TF binding region
ENSG00000142409	Chromatin interaction
ENSG00000223060	Chromatin interaction
ENSG00000167685	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs2631642	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2631652	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs274141	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs274144	0.90[EUR][1000 genomes]
rs274145	0.90[EUR][1000 genomes]
rs274146	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs274151	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs274154	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs274156	0.89[CEU][hapmap]
rs274159	0.89[CEU][hapmap]
rs274163	0.89[CEU][hapmap]
rs274165	0.85[CEU][hapmap]
rs274168	1.00[LWK][hapmap]
rs274177	0.82[EUR][1000 genomes]
rs274180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs274181	0.82[EUR][1000 genomes]
rs3103059	0.90[EUR][1000 genomes]
rs3103060	0.90[EUR][1000 genomes]
rs477807	0.81[EUR][1000 genomes]
rs480528	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs481291	0.87[EUR][1000 genomes]
rs487922	0.90[EUR][1000 genomes]
rs488196	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs565171	0.87[EUR][1000 genomes]
rs581486	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61283021	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs650832	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs652204	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs671061	0.87[EUR][1000 genomes]
rs679082	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs901476	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56653400-56657200	Enhancers	Primary hematopoietic stem cells	blood
2	chr19:56653400-56657600	Weak transcription	Ovary	ovary
3	chr19:56653400-56661200	Weak transcription	Psoas Muscle	Psoas
4	chr19:56653600-56657000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:56653600-56658200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr19:56653600-56658600	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr19:56653600-56659000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr19:56653800-56656400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr19:56653800-56657000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:56653800-56658200	Weak transcription	NHLF	lung
11	chr19:56653800-56658400	Weak transcription	Aorta	Aorta
12	chr19:56653800-56658600	Weak transcription	Primary B cells from peripheral blood	blood
13	chr19:56653800-56658600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr19:56653800-56659000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr19:56653800-56660200	Weak transcription	Primary B cells from cord blood	blood
16	chr19:56653800-56660400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr19:56653800-56661200	Weak transcription	HSMMtube	muscle
18	chr19:56653800-56664200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr19:56653800-56664200	Weak transcription	HUVEC	blood vessel
20	chr19:56653800-56667200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr19:56653800-56669200	Weak transcription	HSMM	muscle
22	chr19:56653800-56669400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr19:56653800-56673000	Weak transcription	Hela-S3	cervix
24	chr19:56653800-56674000	Weak transcription	Fetal Kidney	kidney
25	chr19:56654000-56657000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr19:56654000-56657200	Weak transcription	Brain Germinal Matrix	brain
27	chr19:56654000-56657200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr19:56654000-56658000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr19:56654000-56658400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr19:56654000-56658400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr19:56654000-56658400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:56654000-56658600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr19:56654000-56658600	Weak transcription	Brain Angular Gyrus	brain
34	chr19:56654000-56661000	Weak transcription	Fetal Brain Male	brain
35	chr19:56654000-56662000	Strong transcription	Fetal Stomach	stomach
36	chr19:56654000-56681600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:56654200-56656400	Enhancers	Fetal Intestine Large	intestine
38	chr19:56654200-56656600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr19:56654200-56656800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:56654200-56657000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:56654200-56657000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr19:56654200-56657000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:56654200-56657200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr19:56654200-56657400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr19:56654200-56657600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr19:56654200-56657600	Genic enhancers	Fetal Intestine Small	intestine
47	chr19:56654200-56657800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr19:56654200-56658400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr19:56654200-56658600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr19:56654200-56658600	Weak transcription	Brain Substantia Nigra	brain

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