Variant report

Variant	rs274180
Chromosome Location	chr19:56657331-56657332
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:56657263-56657911	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:56657314-56657681	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56629946..56632652-chr19:56657182..56659175,2	K562	blood:
2	chr19:56629015..56635457-chr19:56649954..56657591,25	MCF-7	breast:
3	chr19:56168627..56170843-chr19:56657131..56658872,2	MCF-7	breast:
4	chr19:56657267..56658891-chr19:56660512..56663390,2	K562	blood:

Variant related genes	Relation type
ZNF444	TF binding region
ENSG00000204533	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000142409	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2631642	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[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];0.85[ASN][1000 genomes]
rs274151	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs274154	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs274177	0.82[EUR][1000 genomes]
rs274181	0.82[EUR][1000 genomes]
rs274182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.84[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];0.85[ASN][1000 genomes]
rs901476	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	chr19:56653400-56657600	Weak transcription	Ovary	ovary
2	chr19:56653400-56661200	Weak transcription	Psoas Muscle	Psoas
3	chr19:56653600-56658200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr19:56653600-56658600	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr19:56653600-56659000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr19:56653800-56658200	Weak transcription	NHLF	lung
7	chr19:56653800-56658400	Weak transcription	Aorta	Aorta
8	chr19:56653800-56658600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr19:56653800-56658600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr19:56653800-56659000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr19:56653800-56660200	Weak transcription	Primary B cells from cord blood	blood
12	chr19:56653800-56660400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr19:56653800-56661200	Weak transcription	HSMMtube	muscle
14	chr19:56653800-56664200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr19:56653800-56664200	Weak transcription	HUVEC	blood vessel
16	chr19:56653800-56667200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:56653800-56669200	Weak transcription	HSMM	muscle
18	chr19:56653800-56669400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr19:56653800-56673000	Weak transcription	Hela-S3	cervix
20	chr19:56653800-56674000	Weak transcription	Fetal Kidney	kidney
21	chr19:56654000-56658000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr19:56654000-56658400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr19:56654000-56658400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr19:56654000-56658400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr19:56654000-56658600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr19:56654000-56658600	Weak transcription	Brain Angular Gyrus	brain
27	chr19:56654000-56661000	Weak transcription	Fetal Brain Male	brain
28	chr19:56654000-56662000	Strong transcription	Fetal Stomach	stomach
29	chr19:56654000-56681600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:56654200-56657400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:56654200-56657600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:56654200-56657600	Genic enhancers	Fetal Intestine Small	intestine
33	chr19:56654200-56657800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr19:56654200-56658400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr19:56654200-56658600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr19:56654200-56658600	Weak transcription	Brain Substantia Nigra	brain
37	chr19:56654200-56658800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr19:56654200-56658800	Weak transcription	Colon Smooth Muscle	Colon
39	chr19:56654200-56663200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr19:56654200-56674000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr19:56654400-56657400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr19:56654400-56658200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr19:56654400-56668400	Weak transcription	HMEC	breast
44	chr19:56654400-56671200	Weak transcription	Small Intestine	intestine
45	chr19:56654600-56658200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr19:56654600-56658200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr19:56654600-56658200	Weak transcription	Esophagus	oesophagus
48	chr19:56654600-56658400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr19:56654600-56658600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr19:56654600-56658600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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