Variant report

Variant	rs28449839
Chromosome Location	chr19:56210352-56210353
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56194595..56204961-chr19:56206160..56210902,10	K562	blood:
2	chr19:56204403..56206705-chr19:56209102..56212375,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267117	Chromatin interaction
ENSG00000063245	Chromatin interaction
ENSG00000211571	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10410886	0.88[AFR][1000 genomes]
rs10419814	0.91[ASN][1000 genomes]
rs310445	0.82[ASN][1000 genomes]
rs73615219	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
6	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv1061024	chr19:56167101-56217359	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	esv3402814	chr19:56210240-56213138	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56188200-56218200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:56188400-56211200	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr19:56188400-56213600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:56188600-56212400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:56188600-56215600	Weak transcription	Fetal Brain Male	brain
6	chr19:56188800-56212400	Strong transcription	Thymus	Thymus
7	chr19:56189200-56212600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr19:56189400-56212400	Strong transcription	Brain Germinal Matrix	brain
9	chr19:56189600-56213200	Strong transcription	Primary T cells from cord blood	blood
10	chr19:56190000-56212600	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr19:56190200-56212400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:56191000-56212400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:56191800-56218800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:56192000-56214600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr19:56192200-56211200	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr19:56192400-56212400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr19:56192800-56213200	Strong transcription	Adipose Nuclei	Adipose
18	chr19:56193200-56214000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:56193600-56213200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:56193800-56212000	Weak transcription	HSMM	muscle
21	chr19:56195000-56212400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr19:56195400-56217600	Weak transcription	Right Atrium	heart
23	chr19:56197600-56212600	Strong transcription	Lung	lung
24	chr19:56197800-56212400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr19:56199000-56212400	Strong transcription	Liver	Liver
26	chr19:56199200-56210800	Strong transcription	Pancreas	Pancrea
27	chr19:56199200-56214600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr19:56199600-56213200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr19:56199800-56210600	Strong transcription	Right Ventricle	heart
30	chr19:56199800-56212400	Strong transcription	Aorta	Aorta
31	chr19:56200000-56212400	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr19:56200000-56212600	Strong transcription	Stomach Smooth Muscle	stomach
33	chr19:56200000-56213200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:56200000-56216000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr19:56200200-56210800	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr19:56200400-56212600	Strong transcription	Esophagus	oesophagus
37	chr19:56200600-56212200	Strong transcription	Gastric	stomach
38	chr19:56200600-56212600	Strong transcription	Fetal Stomach	stomach
39	chr19:56200800-56212600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:56200800-56212600	Strong transcription	Placenta	Placenta
41	chr19:56200800-56212600	Strong transcription	Ovary	ovary
42	chr19:56201000-56213000	Weak transcription	K562	blood
43	chr19:56201400-56212200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr19:56201400-56212400	Strong transcription	Fetal Muscle Leg	muscle
45	chr19:56201400-56212600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr19:56201400-56212800	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr19:56202000-56212400	Strong transcription	Colonic Mucosa	Colon
48	chr19:56202000-56212400	Strong transcription	Spleen	Spleen
49	chr19:56202200-56212600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr19:56202400-56213000	Strong transcription	Fetal Intestine Small	intestine

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