Variant report

Variant	rs4488583
Chromosome Location	chr19:39355367-39355368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39350563..39353350-chr19:39354978..39358283,3	MCF-7	breast:
2	chr19:39326842..39329688-chr19:39354177..39355882,2	K562	blood:
3	chr19:39355316..39357305-chr19:39358972..39361148,3	MCF-7	breast:
4	chr19:39338783..39344716-chr19:39351762..39356757,15	MCF-7	breast:
5	chr19:39339063..39344846-chr19:39351660..39355862,7	MCF-7	breast:
6	chr19:39355225..39357682-chr19:39363417..39365979,2	MCF-7	breast:
7	chr19:39341098..39344560-chr19:39351786..39356667,5	K562	blood:
8	chr19:39354973..39357076-chr19:39358619..39360688,2	MCF-7	breast:
9	chr19:39328430..39329992-chr19:39354096..39356995,2	MCF-7	breast:
10	chr19:39327808..39329688-chr19:39353305..39355677,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000269050	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000187994	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1078733	1.00[EUR][1000 genomes]
rs11883010	1.00[CEU][hapmap]
rs2403782	1.00[EUR][1000 genomes]
rs73537683	1.00[EUR][1000 genomes]
rs73537686	1.00[EUR][1000 genomes]
rs73930203	1.00[EUR][1000 genomes]
rs73930212	1.00[EUR][1000 genomes]
rs73933060	1.00[EUR][1000 genomes]
rs73933061	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4488583	LGALS14	cis	lymphoblastoid	seeQTL
rs4488583	CLC	cis	lymphoblastoid	seeQTL

Chromatin state (count:70 , 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	chr19:39348600-39355400	Enhancers	Primary B cells from peripheral blood	blood
4	chr19:39348600-39359600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:39349000-39355400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:39349400-39359800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:39352400-39355400	Enhancers	Fetal Muscle Leg	muscle
8	chr19:39352400-39356600	Enhancers	Fetal Muscle Trunk	muscle
9	chr19:39352400-39357000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:39352800-39357200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr19:39353200-39358000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr19:39353400-39357800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr19:39353400-39359600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr19:39353400-39363800	Weak transcription	HSMMtube	muscle
15	chr19:39353600-39356200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr19:39353600-39356600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr19:39353600-39356600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:39353600-39357000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr19:39353600-39359200	Weak transcription	Esophagus	oesophagus
20	chr19:39353600-39359600	Weak transcription	Liver	Liver
21	chr19:39353600-39359600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr19:39353600-39359800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr19:39353600-39359800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:39353600-39359800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr19:39353600-39359800	Weak transcription	Colonic Mucosa	Colon
26	chr19:39353600-39359800	Weak transcription	Fetal Lung	lung
27	chr19:39353600-39359800	Weak transcription	Lung	lung
28	chr19:39353800-39357000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr19:39354000-39355600	Weak transcription	Fetal Intestine Large	intestine
30	chr19:39354000-39356800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr19:39354000-39356800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr19:39354000-39359000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:39354000-39359200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr19:39354000-39359600	Weak transcription	Right Atrium	heart
35	chr19:39354000-39359800	Weak transcription	Psoas Muscle	Psoas
36	chr19:39354000-39359800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr19:39354200-39355800	Enhancers	Primary T cells fromperipheralblood	blood
38	chr19:39354200-39356600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr19:39354200-39357200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr19:39354200-39357600	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr19:39354400-39355400	Weak transcription	K562	blood
42	chr19:39354400-39359800	Weak transcription	Left Ventricle	heart
43	chr19:39354600-39355600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr19:39354800-39356200	Enhancers	HUVEC	blood vessel
45	chr19:39354800-39356800	Enhancers	Adipose Nuclei	Adipose
46	chr19:39354800-39357000	Enhancers	Placenta	Placenta
47	chr19:39354800-39358000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr19:39355000-39355400	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr19:39355000-39355800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:39355000-39356000	Enhancers	Hela-S3	cervix

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