Variant report

Variant	rs55876653
Chromosome Location	chr19:39146780-39146781
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39145602..39147315-chr19:39192436..39195321,2	K562	blood:
2	chr19:39145322..39147138-chr19:39167386..39170239,2	K562	blood:
3	chr19:39144043..39146811-chr19:39176683..39178531,2	MCF-7	breast:
4	chr19:39145586..39147740-chr19:39150423..39154465,3	K562	blood:
5	chr19:39146061..39150470-chr19:39339841..39342984,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10403540	0.85[ASN][1000 genomes]
rs10404257	0.93[ASN][1000 genomes]
rs10406778	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10415219	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415646	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10421560	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11083475	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12460849	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12462270	0.82[ASN][1000 genomes]
rs13343794	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13344413	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs16972767	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279144	0.82[ASN][1000 genomes]
rs2303040	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28488032	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28624276	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3745859	0.83[ASN][1000 genomes]
rs3786835	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3786839	0.83[EUR][1000 genomes]
rs3786845	0.82[ASN][1000 genomes]
rs3786848	0.84[ASN][1000 genomes]
rs3786851	0.83[ASN][1000 genomes]
rs3810341	0.98[ASN][1000 genomes]
rs56113315	0.80[EUR][1000 genomes]
rs56365761	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62121814	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62121816	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62121818	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7251903	0.81[EUR][1000 genomes]
rs7252589	0.86[ASN][1000 genomes]
rs7254100	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8111746	0.83[ASN][1000 genomes]
rs883433	0.84[ASN][1000 genomes]
rs979971	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs979972	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39138600-39152200	Transcr. at gene 5' and 3'	A549	lung
2	chr19:39140400-39146800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:39140600-39151000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr19:39141200-39147000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr19:39141200-39147600	Enhancers	Primary hematopoietic stem cells	blood
6	chr19:39141200-39148600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:39141200-39148800	Enhancers	Placenta Amnion	Placenta Amnion
8	chr19:39141200-39162800	Enhancers	Psoas Muscle	Psoas
9	chr19:39141400-39147000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:39141400-39147800	Enhancers	Small Intestine	intestine
11	chr19:39141400-39148000	Genic enhancers	Fetal Muscle Leg	muscle
12	chr19:39141800-39146800	Enhancers	Fetal Lung	lung
13	chr19:39141800-39147200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:39142000-39147000	Enhancers	Brain Angular Gyrus	brain
15	chr19:39142000-39149400	Enhancers	Liver	Liver
16	chr19:39142200-39146800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr19:39142200-39151800	Enhancers	Brain Cingulate Gyrus	brain
18	chr19:39142400-39149400	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr19:39142600-39150400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:39142800-39151200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:39143000-39149800	Enhancers	H9 Cell Line	embryonic stem cell
22	chr19:39143200-39146800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:39143400-39146800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:39143400-39148400	Enhancers	Brain Substantia Nigra	brain
25	chr19:39143400-39149200	Enhancers	Brain Hippocampus Middle	brain
26	chr19:39143400-39150600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:39143400-39154400	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr19:39143800-39147600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:39143800-39148600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr19:39143800-39153200	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr19:39144000-39146800	Genic enhancers	HMEC	breast
32	chr19:39144000-39147000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr19:39144000-39150200	Enhancers	Colon Smooth Muscle	Colon
34	chr19:39144200-39150400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr19:39144200-39153400	Genic enhancers	K562	blood
36	chr19:39144400-39146800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:39144400-39147600	Genic enhancers	NHDF-Ad	bronchial
38	chr19:39144400-39147800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr19:39144400-39148200	Weak transcription	Primary B cells from cord blood	blood
40	chr19:39144400-39148600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
41	chr19:39144400-39150600	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr19:39144400-39152200	Enhancers	Right Ventricle	heart
43	chr19:39144600-39147600	Genic enhancers	Muscle Satellite Cultured Cells	--
44	chr19:39144600-39147600	Genic enhancers	HUVEC	blood vessel
45	chr19:39144600-39147800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr19:39144600-39149000	Genic enhancers	HepG2	liver
47	chr19:39144600-39149600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr19:39144600-39154000	Enhancers	Right Atrium	heart
49	chr19:39144800-39146800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:39144800-39146800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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