Variant report

Variant	rs10413309
Chromosome Location	chr19:19456925-19456926
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19456690-19457023	GM12892	blood:	n/a	n/a
2	MAFK	chr19:19456841-19457190	HepG2	liver:	n/a	chr19:19457014-19457029 chr19:19457016-19457025 chr19:19457015-19457025 chr19:19457011-19457027 chr19:19457012-19457026 chr19:19457009-19457029
3	POLR2A	chr19:19456708-19457187	Hela-S3	cervix:	n/a	n/a
4	MAFK	chr19:19456891-19457080	IMR90	lung:	n/a	chr19:19457014-19457029 chr19:19457016-19457025 chr19:19457015-19457025 chr19:19457011-19457027 chr19:19457012-19457026 chr19:19457009-19457029
5	MAFK	chr19:19456839-19457196	HepG2	liver:	n/a	chr19:19457014-19457029 chr19:19457016-19457025 chr19:19457015-19457025 chr19:19457011-19457027 chr19:19457012-19457026 chr19:19457009-19457029
6	POLR2A	chr19:19456734-19457060	K562	blood:	n/a	n/a
7	POLR2A	chr19:19456925-19457034	K562	blood:	n/a	n/a
8	POLR2A	chr19:19456886-19457160	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr19:19456921-19457212	HepG2	liver:	n/a	n/a
10	MAFF	chr19:19456894-19457100	HepG2	liver:	n/a	chr19:19457013-19457031 chr19:19457012-19457026
11	POLR2A	chr19:19456663-19457167	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:19456762-19457165	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:19456893-19457004	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr19:19456833-19457030	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19453934..19460273-chr19:19460288..19468289,13	K562	blood:
2	chr19:19431656..19433279-chr19:19456145..19458493,2	K562	blood:
3	chr19:19453346..19455308-chr19:19455339..19457866,2	K562	blood:
4	chr19:19456159..19458001-chr19:19462713..19465348,2	MCF-7	breast:
5	chr19:19430396..19433402-chr19:19454872..19458235,4	MCF-7	breast:

Variant related genes	Relation type
MAU2	TF binding region
ENSG00000129933	Chromatin interaction
ENSG00000105705	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10402799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408216	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10417312	0.89[AMR][1000 genomes]
rs10417715	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10422331	0.82[AFR][1000 genomes]
rs10422522	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10422620	0.82[AFR][1000 genomes]
rs10423747	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12327663	0.96[AFR][1000 genomes]
rs16996031	0.96[AFR][1000 genomes]
rs16996042	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2106699	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2315280	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28437425	0.92[AFR][1000 genomes]
rs28857503	0.92[AFR][1000 genomes]
rs55877107	0.85[AFR][1000 genomes]
rs56304704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56317107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60860168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7248765	1.00[AMR][1000 genomes]
rs7249940	1.00[AMR][1000 genomes]
rs73922864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73922870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8110508	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1056419	chr19:19421218-19510611	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19433400-19469800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:19433400-19470600	Strong transcription	Fetal Stomach	stomach
3	chr19:19433800-19468400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr19:19433800-19469800	Strong transcription	Fetal Intestine Large	intestine
5	chr19:19433800-19470400	Strong transcription	Placenta	Placenta
6	chr19:19434200-19469000	Strong transcription	Fetal Thymus	thymus
7	chr19:19434200-19469800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:19434200-19469800	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr19:19434600-19466000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:19434800-19470600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:19435000-19471000	Strong transcription	Fetal Brain Female	brain
12	chr19:19435600-19468600	Strong transcription	Dnd41	blood
13	chr19:19435600-19470400	Strong transcription	Brain Germinal Matrix	brain
14	chr19:19435600-19477600	Weak transcription	Fetal Heart	heart
15	chr19:19436000-19460600	Strong transcription	Brain Cingulate Gyrus	brain
16	chr19:19438200-19469600	Strong transcription	Thymus	Thymus
17	chr19:19438600-19460800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:19438800-19468800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr19:19439600-19461000	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr19:19439600-19469800	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr19:19440000-19470400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr19:19440400-19468400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr19:19440400-19468600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr19:19440400-19469000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:19440400-19469000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr19:19440400-19469200	Strong transcription	Lung	lung
27	chr19:19440400-19469400	Strong transcription	Liver	Liver
28	chr19:19440400-19475400	Weak transcription	Right Atrium	heart
29	chr19:19440600-19468400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr19:19440600-19468800	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr19:19440800-19468600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr19:19440800-19470400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr19:19440800-19470600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr19:19441200-19468600	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr19:19441600-19470400	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr19:19441800-19460800	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr19:19444600-19460800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:19445200-19468000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr19:19446000-19468000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:19446600-19470800	Strong transcription	Fetal Intestine Small	intestine
41	chr19:19446800-19467400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr19:19447200-19467400	Strong transcription	Fetal Muscle Leg	muscle
43	chr19:19448000-19468600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:19449000-19469800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:19449200-19458600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr19:19449200-19470000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:19449400-19458800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:19449400-19458800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:19449400-19469000	Strong transcription	Adipose Nuclei	Adipose
50	chr19:19449800-19468600	Weak transcription	Fetal Brain Male	brain

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