Variant report

Variant	rs11879553
Chromosome Location	chr19:38648609-38648610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38642798..38644805-chr19:38646694..38649003,2	K562	blood:
2	chr19:38645825..38649428-chr19:38653343..38656311,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10426091	1.00[TSI][hapmap]
rs11880776	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11881136	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11881503	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11882737	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1654370	0.92[LWK][hapmap];0.86[MKK][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes]
rs16978902	1.00[EUR][1000 genomes]
rs1725455	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1725457	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35447904	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56140434	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57771568	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57910731	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58352573	0.91[AMR][1000 genomes]
rs58512019	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60625383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs705490	1.00[EUR][1000 genomes]
rs705498	1.00[EUR][1000 genomes]
rs7248658	1.00[EUR][1000 genomes]
rs7255196	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7257055	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257668	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73627606	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73627608	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73627652	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73627672	0.91[AMR][1000 genomes]
rs73627675	0.91[AMR][1000 genomes]
rs73628634	1.00[EUR][1000 genomes]
rs73934104	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8100265	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8100641	0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8100668	1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8101927	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8104392	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105919	1.00[EUR][1000 genomes]
rs8107346	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8110434	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8112492	1.00[EUR][1000 genomes]
rs8112893	1.00[EUR][1000 genomes]
rs8113411	1.00[EUR][1000 genomes]
rs855615	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs855616	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs855626	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38600600-38652800	Weak transcription	NHDF-Ad	bronchial
2	chr19:38611000-38652800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:38611600-38653000	Weak transcription	HUVEC	blood vessel
4	chr19:38611800-38653000	Weak transcription	Fetal Kidney	kidney
5	chr19:38613800-38652200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr19:38613800-38652600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr19:38616000-38652600	Strong transcription	Primary B cells from peripheral blood	blood
8	chr19:38617000-38652000	Strong transcription	Fetal Intestine Small	intestine
9	chr19:38618200-38651000	Strong transcription	Fetal Intestine Large	intestine
10	chr19:38624400-38652400	Weak transcription	Fetal Thymus	thymus
11	chr19:38626400-38652200	Strong transcription	A549	lung
12	chr19:38627000-38652400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:38628400-38652600	Weak transcription	Right Atrium	heart
14	chr19:38628800-38651200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:38629200-38652600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:38629600-38651600	Strong transcription	GM12878-XiMat	blood
17	chr19:38633000-38651000	Strong transcription	Primary B cells from cord blood	blood
18	chr19:38633000-38652400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr19:38633200-38652800	Weak transcription	Colon Smooth Muscle	Colon
20	chr19:38633400-38650800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:38633400-38653000	Weak transcription	Fetal Brain Male	brain
22	chr19:38635400-38652600	Weak transcription	Stomach Mucosa	stomach
23	chr19:38636600-38652600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr19:38637000-38652400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:38637000-38652800	Weak transcription	Brain Substantia Nigra	brain
26	chr19:38638200-38667200	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr19:38638400-38650600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr19:38641600-38652800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr19:38641800-38649800	Strong transcription	Liver	Liver
30	chr19:38642800-38650600	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr19:38643200-38652600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr19:38643800-38649800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr19:38643800-38650000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr19:38643800-38650400	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr19:38643800-38652600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr19:38643800-38652600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr19:38643800-38652600	Weak transcription	Small Intestine	intestine
38	chr19:38643800-38652800	Weak transcription	Left Ventricle	heart
39	chr19:38643800-38654800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr19:38644000-38649800	Weak transcription	Aorta	Aorta
41	chr19:38644000-38649800	Weak transcription	Ovary	ovary
42	chr19:38644000-38652200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:38644000-38652400	Weak transcription	HepG2	liver
44	chr19:38644000-38652400	Weak transcription	NHEK	skin
45	chr19:38644000-38652800	Weak transcription	Placenta	Placenta
46	chr19:38644000-38659200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr19:38644200-38650000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr19:38644200-38652000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:38644400-38652800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr19:38645000-38649200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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