Variant report

Variant	rs1549933
Chromosome Location	chr19:41871142-41871143
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41869456-41871146	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr19:41869301-41871160	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr19:41870862-41871151	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr19:41870725-41871232	HepG2	liver:	n/a	n/a
5	MAX	chr19:41869070-41871296	A549	lung:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41858281..41860213-chr19:41869974..41872050,2	MCF-7	breast:
2	chr19:41856910..41863042-chr19:41867113..41873191,18	MCF-7	breast:
3	chr19:41870450..41872597-chr19:41951300..41953868,2	K562	blood:
4	chr19:41858489..41863412-chr19:41867730..41871601,11	K562	blood:
5	chr19:41868161..41871707-chr19:41902716..41905358,4	MCF-7	breast:
6	chr19:41869689..41871301-chr19:41934522..41938582,3	MCF-7	breast:
7	chr19:41868336..41871272-chr19:41944233..41948538,5	K562	blood:
8	chr19:41824554..41827469-chr19:41868894..41871689,2	K562	blood:
9	chr19:41868160..41871597-chr19:41899998..41904284,10	K562	blood:
10	chr19:41869853..41871782-chr19:41881681..41884054,2	K562	blood:
11	chr19:41814494..41816860-chr19:41868645..41871305,2	K562	blood:
12	chr19:41816143..41817649-chr19:41870161..41871689,2	MCF-7	breast:

No data

Variant related genes	Relation type
B9D2	TF binding region
ENSG00000255730	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000268987	Chromatin interaction
ENSG00000077348	Chromatin interaction
ENSG00000105341	Chromatin interaction
ENSG00000248098	Chromatin interaction
ENSG00000142046	Chromatin interaction
ENSG00000142039	Chromatin interaction
ENSG00000177191	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1025497	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11083616	0.98[ASN][1000 genomes]
rs11083617	0.98[ASN][1000 genomes]
rs11666933	0.95[ASN][1000 genomes]
rs11668109	0.83[AMR][1000 genomes]
rs11670143	0.97[ASN][1000 genomes]
rs12462166	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12983775	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1800469	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1800470	0.92[ASN][1000 genomes]
rs1963413	0.99[ASN][1000 genomes]
rs1982072	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241712	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241713	0.98[ASN][1000 genomes]
rs2241714	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241715	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2317130	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803457	0.94[ASN][1000 genomes]
rs4803458	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4803459	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9797885	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521311	chr19:41856886-41882712	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1549933	CTC-435M10.6	cis	Whole Blood	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41869400-41871200	Active TSS	Brain Germinal Matrix	brain
2	chr19:41869600-41871200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr19:41869600-41871200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr19:41869600-41871200	Active TSS	Colonic Mucosa	Colon
5	chr19:41869600-41871200	Active TSS	GM12878-XiMat	blood
6	chr19:41870200-41871200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
7	chr19:41870200-41871200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr19:41870200-41871200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:41870200-41871200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:41870200-41871200	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr19:41870200-41871200	Flanking Active TSS	Dnd41	blood
12	chr19:41870200-41871400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr19:41870200-41871800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr19:41870400-41871200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:41870400-41871200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr19:41870400-41871200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:41870400-41871200	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr19:41870400-41871400	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr19:41870600-41871200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:41870600-41871200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:41870600-41871200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr19:41870600-41871200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:41870600-41871200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr19:41870600-41871200	Enhancers	Left Ventricle	heart
25	chr19:41870600-41871200	Enhancers	Lung	lung
26	chr19:41870600-41871200	Enhancers	Spleen	Spleen
27	chr19:41870600-41871200	Flanking Active TSS	A549	lung
28	chr19:41870600-41882000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr19:41870800-41871200	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr19:41870800-41871200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:41870800-41871200	Enhancers	Primary B cells from peripheral blood	blood
32	chr19:41870800-41871200	Enhancers	Primary T cells fromperipheralblood	blood
33	chr19:41870800-41871200	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr19:41870800-41871200	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr19:41870800-41871200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr19:41870800-41871200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr19:41870800-41871200	Enhancers	Fetal Intestine Large	intestine
38	chr19:41870800-41871200	Enhancers	Fetal Muscle Trunk	muscle
39	chr19:41870800-41871200	Enhancers	Fetal Stomach	stomach
40	chr19:41870800-41871200	Enhancers	Gastric	stomach
41	chr19:41870800-41871200	Enhancers	Pancreas	Pancrea
42	chr19:41870800-41871200	Enhancers	Psoas Muscle	Psoas
43	chr19:41870800-41871200	Enhancers	Right Atrium	heart
44	chr19:41870800-41871200	Enhancers	Right Ventricle	heart
45	chr19:41870800-41871200	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr19:41870800-41871200	Enhancers	Thymus	Thymus
47	chr19:41870800-41871200	Flanking Active TSS	K562	blood
48	chr19:41870800-41871400	Enhancers	Primary hematopoietic stem cells	blood
49	chr19:41870800-41874000	Weak transcription	Esophagus	oesophagus
50	chr19:41870800-41874000	Weak transcription	Small Intestine	intestine

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