Variant report

Variant	rs901476
Chromosome Location	chr19:56664539-56664540
allele	C/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	CTCF	chr19:56664432-56664539	H1-hESC	embryonic stem cell:	n/a	chr19:56664492-56664505 chr19:56664489-56664507
2	CTCF	chr19:56664500-56664650	AoAF	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56653375..56656059-chr19:56663950..56668428,4	MCF-7	breast:
2	chr19:56653169..56655631-chr19:56663595..56666342,4	MCF-7	breast:

Variant related genes	Relation type
ZNF444	TF binding region
ENSG00000204533	TF binding region
ENSG00000167685	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs2631642	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2631652	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs274141	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs274144	0.90[EUR][1000 genomes]
rs274145	0.90[EUR][1000 genomes]
rs274146	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs274151	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs274154	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs274155	0.82[CHB][hapmap]
rs274156	0.89[CEU][hapmap]
rs274159	0.90[CEU][hapmap]
rs274163	0.90[CEU][hapmap]
rs274165	0.86[CEU][hapmap]
rs274168	0.85[MEX][hapmap]
rs274180	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs274182	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]
rs3103059	0.90[EUR][1000 genomes]
rs3103060	0.90[EUR][1000 genomes]
rs477807	0.81[EUR][1000 genomes]
rs480528	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs481291	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs487922	0.90[EUR][1000 genomes]
rs488196	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs565171	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs581486	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61283021	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs650832	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs652204	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs671061	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs679082	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56653800-56667200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:56653800-56669200	Weak transcription	HSMM	muscle
3	chr19:56653800-56669400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr19:56653800-56673000	Weak transcription	Hela-S3	cervix
5	chr19:56653800-56674000	Weak transcription	Fetal Kidney	kidney
6	chr19:56654000-56681600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:56654200-56674000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr19:56654400-56668400	Weak transcription	HMEC	breast
9	chr19:56654400-56671200	Weak transcription	Small Intestine	intestine
10	chr19:56655200-56672200	Weak transcription	NHDF-Ad	bronchial
11	chr19:56656400-56664800	Weak transcription	K562	blood
12	chr19:56656400-56667400	Weak transcription	Stomach Mucosa	stomach
13	chr19:56656400-56672200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr19:56659200-56673000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr19:56659400-56664600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:56659400-56667200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr19:56659400-56671000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr19:56659600-56670400	Weak transcription	NHEK	skin
19	chr19:56660000-56668000	Weak transcription	Colonic Mucosa	Colon
20	chr19:56660200-56664600	Weak transcription	Aorta	Aorta
21	chr19:56660200-56666000	Weak transcription	NHLF	lung
22	chr19:56660200-56670400	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr19:56660400-56664600	Weak transcription	Spleen	Spleen
24	chr19:56660400-56666000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr19:56660400-56666400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr19:56660400-56666800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr19:56660400-56667200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr19:56660600-56665400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr19:56661400-56665400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr19:56661400-56676200	Weak transcription	Fetal Brain Male	brain
31	chr19:56661600-56664800	Weak transcription	Esophagus	oesophagus
32	chr19:56661600-56665400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:56661600-56665400	Weak transcription	Fetal Brain Female	brain
34	chr19:56661600-56666000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr19:56661600-56666000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:56661600-56666000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr19:56661600-56666000	Weak transcription	Placenta	Placenta
38	chr19:56661600-56666000	Weak transcription	Right Ventricle	heart
39	chr19:56661600-56666200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr19:56661600-56666200	Weak transcription	Brain Hippocampus Middle	brain
41	chr19:56661600-56666400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:56661600-56667400	Weak transcription	Brain Substantia Nigra	brain
43	chr19:56661600-56668400	Weak transcription	Right Atrium	heart
44	chr19:56661600-56669200	Weak transcription	Brain Angular Gyrus	brain
45	chr19:56661800-56665200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr19:56661800-56666000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:56661800-56666000	Weak transcription	A549	lung
48	chr19:56661800-56666000	Weak transcription	GM12878-XiMat	blood
49	chr19:56661800-56666200	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr19:56661800-56666800	Weak transcription	Osteobl	bone

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