Variant report

Variant	rs2061779
Chromosome Location	chr19:38084659-38084660
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:38084545-38084716	HepG2	liver:	n/a	n/a
2	SREBP1	chr19:38084608-38086685	GM12878	blood:	n/a	n/a
3	MXI1	chr19:38084639-38086744	IMR90	lung:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38077508..38079095-chr19:38083626..38085233,2	K562	blood:
2	chr19:38084603..38087452-chr19:38269351..38271925,3	MCF-7	breast:
3	chr19:38083796..38085329-chr19:38149997..38151871,2	MCF-7	breast:
4	chr19:38083812..38086216-chr19:38209948..38211806,2	MCF-7	breast:
5	chr19:38083351..38084930-chr19:38145695..38147583,2	K562	blood:
6	chr19:38083338..38085691-chr19:38270478..38272116,2	K562	blood:
7	chr19:38078147..38079812-chr19:38083382..38085459,2	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF540	TF binding region
ENSG00000198182	Chromatin interaction
ENSG00000120784	Chromatin interaction
ENSG00000189144	Chromatin interaction
ENSG00000267422	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1016291	1.00[AFR][1000 genomes]
rs16958869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16972326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16973130	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs16973541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16973717	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16973886	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16973890	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16973919	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16974061	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16974358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16975375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16975696	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs16975712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16975753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16975859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2045907	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2290998	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2306200	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2385128	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3795068	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3795070	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs41325249	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4330033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4452074	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs73632242	0.88[ASN][1000 genomes]
rs8107454	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8108032	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs955711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[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:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38083600-38085400	ZNF genes & repeats	A549	lung
2	chr19:38083800-38084800	Weak transcription	Fetal Brain Male	brain
3	chr19:38084400-38084800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr19:38084400-38085000	Enhancers	Left Ventricle	heart
5	chr19:38084400-38085000	Enhancers	Spleen	Spleen
6	chr19:38084400-38085200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:38084400-38085200	Flanking Active TSS	Dnd41	blood
8	chr19:38084400-38085400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr19:38084400-38086000	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr19:38084400-38086200	Active TSS	NHEK	skin
11	chr19:38084400-38086400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:38084400-38086400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr19:38084600-38084800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:38084600-38084800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:38084600-38084800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr19:38084600-38084800	Enhancers	Primary B cells from cord blood	blood
17	chr19:38084600-38084800	Enhancers	Primary B cells from peripheral blood	blood
18	chr19:38084600-38084800	Enhancers	Primary T cells fromperipheralblood	blood
19	chr19:38084600-38084800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr19:38084600-38084800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:38084600-38084800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
22	chr19:38084600-38084800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr19:38084600-38084800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr19:38084600-38084800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr19:38084600-38084800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr19:38084600-38084800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:38084600-38084800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:38084600-38084800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr19:38084600-38084800	Enhancers	Aorta	Aorta
30	chr19:38084600-38084800	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr19:38084600-38084800	Active TSS	Fetal Lung	lung
32	chr19:38084600-38084800	Enhancers	Fetal Thymus	thymus
33	chr19:38084600-38084800	Enhancers	Ovary	ovary
34	chr19:38084600-38084800	Flanking Active TSS	Pancreas	Pancrea
35	chr19:38084600-38084800	Flanking Active TSS	Placenta Amnion	Placenta Amnion
36	chr19:38084600-38084800	Enhancers	Right Ventricle	heart
37	chr19:38084600-38084800	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr19:38084600-38084800	Enhancers	Stomach Mucosa	stomach
39	chr19:38084600-38084800	Enhancers	Thymus	Thymus
40	chr19:38084600-38084800	Flanking Active TSS	HepG2	liver
41	chr19:38084600-38084800	Enhancers	HSMMtube	muscle
42	chr19:38084600-38084800	Enhancers	NH-A	brain
43	chr19:38084600-38084800	Active TSS	NHDF-Ad	bronchial
44	chr19:38084600-38084800	Active TSS	Osteobl	bone
45	chr19:38084600-38085000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr19:38084600-38085000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr19:38084600-38085000	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr19:38084600-38085000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:38084600-38085000	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr19:38084600-38085000	Flanking Active TSS	Brain Cingulate Gyrus	brain

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