Variant report

Variant	rs62108289
Chromosome Location	chr19:38145435-38145436
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38145174..38146985-chr19:38184008..38186251,2	MCF-7	breast:
2	chr19:38085961..38087829-chr19:38145172..38147580,2	K562	blood:
3	chr19:37957663..37960695-chr19:38143642..38147199,3	MCF-7	breast:
4	chr19:37960304..37962188-chr19:38144303..38146867,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196437	Chromatin interaction
ENSG00000171817	Chromatin interaction
ENSG00000267319	Chromatin interaction
ENSG00000171827	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10153500	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10424047	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11083424	0.82[AMR][1000 genomes]
rs11878261	0.81[EUR][1000 genomes]
rs11879149	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880056	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11880604	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11883255	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2891683	0.80[AFR][1000 genomes]
rs2927744	0.80[AFR][1000 genomes]
rs34206817	1.00[EUR][1000 genomes]
rs34743484	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3810359	1.00[ASN][1000 genomes]
rs45505797	0.83[EUR][1000 genomes]
rs4802069	0.81[AFR][1000 genomes]
rs56075341	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56264690	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56281742	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57504517	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57725815	0.93[EUR][1000 genomes]
rs57867853	1.00[EUR][1000 genomes]
rs59966837	1.00[EUR][1000 genomes]
rs60686304	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62108260	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62108262	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62108264	1.00[ASN][1000 genomes]
rs62108290	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62108292	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62108293	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62108297	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62108302	0.90[ASN][1000 genomes]
rs62108344	0.87[AFR][1000 genomes]
rs62108348	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62108354	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62110178	1.00[EUR][1000 genomes]
rs62110183	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62110185	0.93[EUR][1000 genomes]
rs62110186	0.93[EUR][1000 genomes]
rs62110187	0.84[EUR][1000 genomes]
rs62110188	0.81[EUR][1000 genomes]
rs62111488	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62111490	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7245981	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7247175	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7258992	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7259029	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7259321	0.82[AMR][1000 genomes]
rs7259717	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73930999	0.83[EUR][1000 genomes]
rs73932929	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73932955	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs8101991	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8102189	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8104124	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8104747	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8108261	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][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	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38144000-38148000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:38144200-38145600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:38144200-38147200	Active TSS	GM12878-XiMat	blood
4	chr19:38144400-38145600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr19:38144400-38146200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:38144400-38147600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:38144600-38145600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
8	chr19:38144600-38145600	Flanking Active TSS	Brain Cingulate Gyrus	brain
9	chr19:38144600-38145600	Flanking Active TSS	Rectal Smooth Muscle	rectum
10	chr19:38144600-38145800	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr19:38144600-38146000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:38144600-38146800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr19:38144600-38147000	Active TSS	A549	lung
14	chr19:38144600-38147200	Active TSS	Fetal Kidney	kidney
15	chr19:38144600-38147400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:38144600-38147400	Active TSS	NHDF-Ad	bronchial
17	chr19:38144600-38147600	Active TSS	Fetal Stomach	stomach
18	chr19:38144600-38147600	Active TSS	Hela-S3	cervix
19	chr19:38144600-38147600	Active TSS	NHLF	lung
20	chr19:38144800-38145600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
21	chr19:38144800-38145600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr19:38144800-38145600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr19:38144800-38145600	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr19:38144800-38145600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr19:38144800-38145800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr19:38144800-38145800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr19:38144800-38145800	Flanking Active TSS	HUVEC	blood vessel
28	chr19:38144800-38146000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
29	chr19:38144800-38146000	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr19:38144800-38146000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr19:38144800-38146200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr19:38144800-38146200	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr19:38144800-38146600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr19:38144800-38147200	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr19:38144800-38147200	Active TSS	Fetal Thymus	thymus
36	chr19:38144800-38147400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:38144800-38147400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr19:38144800-38147400	Active TSS	Left Ventricle	heart
39	chr19:38144800-38147600	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr19:38144800-38147600	Active TSS	H1 Cell Line	embryonic stem cell
41	chr19:38144800-38147600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:38144800-38147600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:38144800-38147600	Active TSS	Fetal Muscle Trunk	muscle
44	chr19:38145000-38145600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr19:38145000-38145800	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr19:38145000-38145800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr19:38145000-38145800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr19:38145000-38146200	Active TSS	Fetal Brain Male	brain
49	chr19:38145000-38147000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr19:38145000-38147000	Active TSS	Right Ventricle	heart

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