Variant report

Variant	rs58399999
Chromosome Location	chr19:39353563-39353564
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39338783..39344716-chr19:39351762..39356757,15	MCF-7	breast:
2	chr19:39339531..39344833-chr19:39351137..39354995,9	K562	blood:
3	chr19:39339063..39344846-chr19:39351660..39355862,7	MCF-7	breast:
4	chr19:39347520..39349434-chr19:39351860..39353901,3	K562	blood:
5	chr19:39341098..39344560-chr19:39351786..39356667,5	K562	blood:
6	chr19:39327808..39329688-chr19:39353305..39355677,2	K562	blood:
7	chr19:39346827..39349071-chr19:39352230..39353984,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10411209	1.00[ASN][1000 genomes]
rs10411301	1.00[ASN][1000 genomes]
rs10423309	1.00[ASN][1000 genomes]
rs11883010	1.00[EUR][1000 genomes]
rs16972885	1.00[ASN][1000 genomes]
rs2070250	1.00[ASN][1000 genomes]
rs2070251	1.00[ASN][1000 genomes]
rs2116853	1.00[ASN][1000 genomes]
rs2163811	1.00[ASN][1000 genomes]
rs2304115	1.00[ASN][1000 genomes]
rs2304116	1.00[ASN][1000 genomes]
rs28362605	1.00[ASN][1000 genomes]
rs3181068	1.00[ASN][1000 genomes]
rs34264048	1.00[ASN][1000 genomes]
rs59849895	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60311832	1.00[EUR][1000 genomes]
rs60524963	0.85[AMR][1000 genomes]
rs61232096	1.00[ASN][1000 genomes]
rs73537679	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73537681	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv911673	chr19:39335274-39365401	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	esv1798153	chr19:39338663-39399277	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39343600-39359800	Weak transcription	Small Intestine	intestine
2	chr19:39344200-39356400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:39347800-39354400	Enhancers	Placenta	Placenta
4	chr19:39348600-39353800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr19:39348600-39355400	Enhancers	Primary B cells from peripheral blood	blood
6	chr19:39348600-39359600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr19:39348800-39355000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr19:39349000-39354200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr19:39349000-39355000	Weak transcription	Primary T cells from cord blood	blood
10	chr19:39349000-39355400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr19:39349400-39359800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:39350400-39354000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr19:39350800-39354200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr19:39350800-39354600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr19:39351800-39354200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr19:39352000-39355000	Enhancers	Primary B cells from cord blood	blood
17	chr19:39352400-39354000	Enhancers	Psoas Muscle	Psoas
18	chr19:39352400-39354400	Enhancers	HUVEC	blood vessel
19	chr19:39352400-39355400	Enhancers	Fetal Muscle Leg	muscle
20	chr19:39352400-39356600	Enhancers	Fetal Muscle Trunk	muscle
21	chr19:39352400-39357000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:39352600-39354000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr19:39352800-39353600	Enhancers	Lung	lung
24	chr19:39352800-39354000	Enhancers	Primary hematopoietic stem cells	blood
25	chr19:39352800-39354200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr19:39352800-39357200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr19:39353000-39353600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr19:39353000-39353600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:39353000-39353600	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr19:39353000-39353600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr19:39353000-39353600	Enhancers	Liver	Liver
32	chr19:39353000-39353600	Enhancers	Colon Smooth Muscle	Colon
33	chr19:39353000-39353600	Enhancers	Esophagus	oesophagus
34	chr19:39353000-39353600	Enhancers	Fetal Lung	lung
35	chr19:39353000-39353600	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr19:39353000-39353600	Enhancers	A549	lung
37	chr19:39353000-39353600	Enhancers	HepG2	liver
38	chr19:39353000-39353600	Enhancers	HSMM	muscle
39	chr19:39353000-39353800	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr19:39353000-39354000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr19:39353000-39354000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr19:39353000-39354000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr19:39353000-39354000	Enhancers	Fetal Intestine Large	intestine
44	chr19:39353000-39354000	Enhancers	Fetal Intestine Small	intestine
45	chr19:39353000-39354000	Enhancers	Fetal Stomach	stomach
46	chr19:39353000-39354000	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr19:39353000-39354000	Enhancers	Stomach Mucosa	stomach
48	chr19:39353000-39354000	Enhancers	Spleen	Spleen
49	chr19:39353000-39354000	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr19:39353000-39354200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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