Variant report

Variant	rs274185
Chromosome Location	chr19:56654609-56654610
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RXRA	chr19:56654483-56654813	HepG2	liver:	n/a	chr19:56654721-56654741
2	POLR2A	chr19:56651742-56655652	HepG2	liver:	n/a	n/a
3	MYBL2	chr19:56653122-56654754	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:56653040-56655313	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:56653031-56655237	HepG2	liver:	n/a	n/a
6	HEY1	chr19:56654195-56654811	HepG2	liver:	n/a	n/a
7	GATA3	chr19:56654512-56655083	MCF-7	breast:	n/a	n/a
8	POLR2A	chr19:56654376-56654640	HepG2	liver:	n/a	n/a
9	HEY1	chr19:56653006-56654765	HepG2	liver:	n/a	n/a
10	POLR2A	chr19:56653443-56654975	HepG2	liver:	n/a	n/a
11	SMC3	chr19:56653468-56654740	HepG2	liver:	n/a	n/a
12	MYC	chr19:56654413-56654831	HepG2	liver:	n/a	n/a
13	MYC	chr19:56654428-56654645	MCF-7	breast:	n/a	n/a
14	MAX	chr19:56653043-56655212	HepG2	liver:	n/a	n/a
15	CHD2	chr19:56654437-56654633	HepG2	liver:	n/a	n/a
16	POLR2A	chr19:56653085-56654705	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56642703..56647128-chr19:56651543..56655262,4	MCF-7	breast:
2	chr19:56615193..56619302-chr19:56653183..56656350,4	MCF-7	breast:
3	chr19:56629015..56635457-chr19:56649954..56657591,25	MCF-7	breast:
4	chr19:56652382..56654278-chr19:56654581..56656087,2	MCF-7	breast:
5	chr19:56654193..56655732-chr19:56826080..56828082,2	MCF-7	breast:
6	chr19:56653169..56655631-chr19:56663595..56666342,4	MCF-7	breast:
7	chr19:56165204..56168088-chr19:56651419..56654921,3	MCF-7	breast:
8	chr19:56629593..56635165-chr19:56650391..56656450,20	K562	blood:
9	chr19:56627257..56634581-chr19:56650310..56656612,28	MCF-7	breast:
10	chr19:55627370..55630159-chr19:56652326..56655281,2	MCF-7	breast:
11	chr19:56653375..56656059-chr19:56663950..56668428,4	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF444	TF binding region
ENSG00000142409	Chromatin interaction
ENSG00000131848	Chromatin interaction
ENSG00000125503	Chromatin interaction
ENSG00000200646	Chromatin interaction
ENSG00000167685	Chromatin interaction
ENSG00000267549	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000223060	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2637084	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2637085	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs274142	0.90[EUR][1000 genomes]
rs274147	0.83[ASN][1000 genomes]
rs274148	0.87[ASN][1000 genomes]
rs274149	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs274150	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs274153	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs274176	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs274178	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]
rs274179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs274184	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs502722	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59180052	0.86[AFR][1000 genomes]
rs679557	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7255998	0.90[YRI][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

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56652000-56654800	Active TSS	Rectal Smooth Muscle	rectum
2	chr19:56653200-56654800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
3	chr19:56653200-56655400	Flanking Active TSS	Liver	Liver
4	chr19:56653400-56655000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
5	chr19:56653400-56655400	Enhancers	Placenta	Placenta
6	chr19:56653400-56657200	Enhancers	Primary hematopoietic stem cells	blood
7	chr19:56653400-56657600	Weak transcription	Ovary	ovary
8	chr19:56653400-56661200	Weak transcription	Psoas Muscle	Psoas
9	chr19:56653600-56654800	Enhancers	Right Atrium	heart
10	chr19:56653600-56654800	Genic enhancers	K562	blood
11	chr19:56653600-56655000	Enhancers	Adipose Nuclei	Adipose
12	chr19:56653600-56655000	Enhancers	Left Ventricle	heart
13	chr19:56653600-56655000	Enhancers	Right Ventricle	heart
14	chr19:56653600-56655200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:56653600-56655800	Enhancers	Primary T cells fromperipheralblood	blood
16	chr19:56653600-56657000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:56653600-56658200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr19:56653600-56658600	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr19:56653600-56659000	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr19:56653800-56654800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr19:56653800-56654800	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr19:56653800-56654800	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr19:56653800-56654800	Enhancers	Colonic Mucosa	Colon
24	chr19:56653800-56654800	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr19:56653800-56655000	Enhancers	Primary T cells from cord blood	blood
26	chr19:56653800-56655000	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr19:56653800-56655000	Enhancers	Fetal Lung	lung
28	chr19:56653800-56655200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr19:56653800-56655200	Enhancers	NHDF-Ad	bronchial
30	chr19:56653800-56655400	Flanking Active TSS	HepG2	liver
31	chr19:56653800-56656400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr19:56653800-56657000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr19:56653800-56658200	Weak transcription	NHLF	lung
34	chr19:56653800-56658400	Weak transcription	Aorta	Aorta
35	chr19:56653800-56658600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr19:56653800-56658600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr19:56653800-56659000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr19:56653800-56660200	Weak transcription	Primary B cells from cord blood	blood
39	chr19:56653800-56660400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr19:56653800-56661200	Weak transcription	HSMMtube	muscle
41	chr19:56653800-56664200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr19:56653800-56664200	Weak transcription	HUVEC	blood vessel
43	chr19:56653800-56667200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr19:56653800-56669200	Weak transcription	HSMM	muscle
45	chr19:56653800-56669400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr19:56653800-56673000	Weak transcription	Hela-S3	cervix
47	chr19:56653800-56674000	Weak transcription	Fetal Kidney	kidney
48	chr19:56654000-56654800	Genic enhancers	GM12878-XiMat	blood
49	chr19:56654000-56655000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:56654000-56655000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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