Variant report

Variant	rs58639706
Chromosome Location	chr19:43968738-43968739
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr19:43966874-43968994	H1-neurons	neurons:	n/a	chr19:43967994-43968007
2	MAX	chr19:43966917-43968790	A549	lung:	n/a	n/a
3	MAZ	chr19:43967257-43968743	K562	blood:	n/a	n/a
4	KAP1	chr19:43968563-43969058	K562	blood:	n/a	n/a
5	POLR2A	chr19:43967098-43968845	MCF-7	breast:	n/a	n/a
6	ZBTB7A	chr19:43967944-43968811	ECC-1	luminal epithelium:	n/a	chr19:43968382-43968389

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:43965066..43971111-chr19:44006791..44009897,14	MCF-7	breast:
2	chr19:43967204..43969877-chr19:44006593..44010322,9	MCF-7	breast:
3	chr19:43966525..43969059-chr19:44008556..44010178,2	K562	blood:
4	chr19:43967559..43969177-chr19:44122484..44124753,2	K562	blood:
5	chr19:43857729..43859549-chr19:43967499..43969532,2	MCF-7	breast:
6	chr19:43968715..43971429-chr19:44172597..44174445,2	MCF-7	breast:
7	chr19:43967717..43971076-chr19:44036987..44039699,3	MCF-7	breast:
8	chr19:43966113..43971089-chr19:44005040..44010546,6	K562	blood:

No data

Variant related genes	Relation type
LYPD3	TF binding region
ENSG00000011422	Chromatin interaction
ENSG00000204936	Chromatin interaction
ENSG00000131116	Chromatin interaction
ENSG00000176472	Chromatin interaction
ENSG00000176531	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs17724968	0.86[ASN][1000 genomes]
rs3746004	1.00[ASN][1000 genomes]
rs3786936	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59764328	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv2501	chr19:43942581-43978424	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:43966800-43969000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
2	chr19:43967000-43968800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:43967000-43968800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:43967000-43968800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
5	chr19:43967000-43968800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr19:43967000-43969000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr19:43967000-43969000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:43967000-43969000	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr19:43967200-43968800	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr19:43967200-43968800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr19:43967200-43968800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr19:43967200-43968800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:43967200-43968800	Flanking Active TSS	Liver	Liver
14	chr19:43967200-43968800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
15	chr19:43967200-43968800	Active TSS	Ovary	ovary
16	chr19:43967200-43968800	Active TSS	Psoas Muscle	Psoas
17	chr19:43967200-43969000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
18	chr19:43967400-43968800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:43967400-43968800	Active TSS	Osteobl	bone
20	chr19:43967400-43970200	Active TSS	Esophagus	oesophagus
21	chr19:43967600-43968800	Active TSS	Brain Angular Gyrus	brain
22	chr19:43967800-43968800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:43967800-43969000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:43967800-43969000	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr19:43967800-43969000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr19:43967800-43969000	Flanking Active TSS	Dnd41	blood
27	chr19:43967800-43969000	Flanking Active TSS	GM12878-XiMat	blood
28	chr19:43968000-43968800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr19:43968000-43968800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr19:43968000-43968800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
31	chr19:43968000-43968800	Bivalent/Poised TSS	Fetal Brain Female	brain
32	chr19:43968000-43968800	Flanking Active TSS	HMEC	breast
33	chr19:43968000-43969000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr19:43968000-43969000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr19:43968000-43970000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr19:43968000-43970000	Flanking Active TSS	Placenta	Placenta
37	chr19:43968200-43968800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
38	chr19:43968200-43968800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr19:43968200-43968800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:43968200-43968800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
41	chr19:43968200-43968800	Flanking Active TSS	Left Ventricle	heart
42	chr19:43968200-43969000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr19:43968200-43969000	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr19:43968200-43969000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr19:43968200-43969000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr19:43968200-43969000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr19:43968200-43969000	Flanking Active TSS	Colonic Mucosa	Colon
48	chr19:43968200-43969000	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr19:43968200-43969000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr19:43968200-43969000	Flanking Active TSS	Stomach Smooth Muscle	stomach

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