Variant report

Variant	rs7250471
Chromosome Location	chr19:56898853-56898854
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56888312..56892282-chr19:56896043..56899237,5	K562	blood:
2	chr19:56896992..56902951-chr19:56903012..56907037,12	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF583-2	chr19:56898781-56899067	ENSG00000267192.1

Variant related genes	Relation type
ENSG00000018869	Chromatin interaction
ENSG00000267459	Chromatin interaction
ENSG00000267454	Chromatin interaction
ENSG00000267776	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10424676	0.81[ASN][1000 genomes]
rs11665972	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1860568	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2288858	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2304124	1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs58129651	0.93[ASN][1000 genomes]
rs7250753	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73621238	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
5	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56881200-56904000	ZNF genes & repeats	Liver	Liver
2	chr19:56889200-56901200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:56889200-56904400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:56889400-56904000	Weak transcription	Fetal Heart	heart
5	chr19:56889400-56904000	Weak transcription	K562	blood
6	chr19:56890000-56900200	Weak transcription	Right Ventricle	heart
7	chr19:56890200-56903600	Weak transcription	Fetal Brain Male	brain
8	chr19:56890600-56900200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr19:56890600-56900400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:56890600-56904000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr19:56893600-56899800	Weak transcription	Placenta	Placenta
12	chr19:56893600-56900000	Weak transcription	Pancreas	Pancrea
13	chr19:56894200-56899000	Weak transcription	Fetal Intestine Large	intestine
14	chr19:56894200-56900800	ZNF genes & repeats	Primary T cells from cord blood	blood
15	chr19:56894200-56903800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:56894400-56899000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
17	chr19:56894600-56899800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr19:56894800-56900000	Weak transcription	Fetal Stomach	stomach
19	chr19:56894800-56902000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
20	chr19:56894800-56902000	Strong transcription	Brain Hippocampus Middle	brain
21	chr19:56894800-56903400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:56895200-56899800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
23	chr19:56895200-56900000	ZNF genes & repeats	Psoas Muscle	Psoas
24	chr19:56895200-56903200	ZNF genes & repeats	Primary B cells from cord blood	blood
25	chr19:56895200-56903400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:56895400-56901200	Weak transcription	Fetal Thymus	thymus
27	chr19:56895400-56902200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:56895400-56902600	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr19:56895800-56900200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:56895800-56902000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:56896000-56899200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr19:56896000-56899200	Strong transcription	Fetal Lung	lung
33	chr19:56896000-56900000	Weak transcription	Brain Angular Gyrus	brain
34	chr19:56896000-56901800	Strong transcription	Brain Substantia Nigra	brain
35	chr19:56896000-56904400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr19:56896200-56901200	Weak transcription	Colon Smooth Muscle	Colon
37	chr19:56896400-56899200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr19:56896400-56899800	Weak transcription	HSMMtube	muscle
39	chr19:56896400-56901200	Weak transcription	Colonic Mucosa	Colon
40	chr19:56896600-56899800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr19:56896600-56900200	Weak transcription	Thymus	Thymus
42	chr19:56896600-56901400	Weak transcription	Fetal Brain Female	brain
43	chr19:56896600-56902000	Strong transcription	Stomach Smooth Muscle	stomach
44	chr19:56896600-56904200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr19:56896800-56900000	Weak transcription	Brain Anterior Caudate	brain
46	chr19:56896800-56900200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr19:56896800-56900400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr19:56896800-56900600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr19:56896800-56900800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr19:56896800-56903800	Weak transcription	Fetal Kidney	kidney

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