Variant report

Variant	rs7249819
Chromosome Location	chr19:40853376-40853377
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:8)
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	ZNF384	chr19:40853376-40853525	K562	blood:	n/a	n/a
2	FOSL2	chr19:40853323-40855470	A549	lung:	n/a	chr19:40854527-40854536 chr19:40854259-40854268
3	ZNF384	chr19:40853304-40853698	GM12878	blood:	n/a	n/a
4	SIX5	chr19:40853344-40855578	A549	lung:	n/a	n/a
5	HCFC1	chr19:40853367-40855133	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:40846921..40852460-chr19:40852861..40856555,6	K562	blood:
2	chr19:40853192..40856646-chr19:40870044..40873206,4	K562	blood:
3	chr19:40853028..40855563-chr19:40876148..40878218,2	K562	blood:
4	chr19:40852692..40855852-chr19:40948280..40952207,5	K562	blood:
5	chr19:40846573..40849159-chr19:40852803..40855284,3	K562	blood:
6	chr19:40853029..40856025-chr19:41082472..41085390,2	K562	blood:
7	chr19:40851266..40855955-chr19:40945466..40950850,6	K562	blood:
8	chr19:40788680..40791212-chr19:40852795..40854366,2	K562	blood:

No data

Variant related genes	Relation type
PLD3	TF binding region
C19orf47	TF binding region
ENSG00000105223	Chromatin interaction
ENSG00000167565	Chromatin interaction
ENSG00000206925	Chromatin interaction
ENSG00000160392	Chromatin interaction
ENSG00000160410	Chromatin interaction
ENSG00000268366	Chromatin interaction
ENSG00000105221	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11666690	0.85[EUR][1000 genomes]
rs11666860	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11667443	0.85[EUR][1000 genomes]
rs11667768	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667774	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668006	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11668520	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11669006	0.85[EUR][1000 genomes]
rs11669332	0.85[EUR][1000 genomes]
rs11670323	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11671439	0.84[EUR][1000 genomes]
rs35090721	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3760636	0.81[ASN][1000 genomes]
rs45441197	0.93[ASN][1000 genomes]
rs45497695	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56672337	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59058760	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59106111	0.84[EUR][1000 genomes]
rs6508937	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66623822	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67587726	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7245751	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73933236	0.82[EUR][1000 genomes]
rs73933237	0.85[EUR][1000 genomes]
rs73933238	0.84[EUR][1000 genomes]
rs73933240	0.85[EUR][1000 genomes]
rs73933241	0.85[EUR][1000 genomes]
rs8105478	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer 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 miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	esv2754051	chr19:40848081-40863842	Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr19:40834400-40853400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:40834800-40853600	Weak transcription	Small Intestine	intestine
3	chr19:40836000-40853600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:40837400-40853400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr19:40837400-40853600	Weak transcription	Stomach Mucosa	stomach
6	chr19:40839800-40853400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:40840000-40853400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr19:40840000-40853600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:40840400-40853400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr19:40842200-40853600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr19:40842200-40853600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:40842400-40853400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr19:40842400-40853600	Weak transcription	Fetal Intestine Large	intestine
14	chr19:40842400-40853600	Weak transcription	Ovary	ovary
15	chr19:40842600-40853400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr19:40842800-40853600	Weak transcription	Pancreas	Pancrea
17	chr19:40843000-40853400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr19:40845600-40853400	Weak transcription	Fetal Lung	lung
19	chr19:40846200-40853400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr19:40848000-40853600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:40848000-40853600	Weak transcription	Colonic Mucosa	Colon
22	chr19:40848000-40853600	Weak transcription	Thymus	Thymus
23	chr19:40848200-40853400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:40848200-40853600	Weak transcription	Fetal Intestine Small	intestine
25	chr19:40848400-40853800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr19:40848800-40853400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr19:40849000-40853400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr19:40849600-40853600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr19:40851000-40853400	Weak transcription	HSMMtube	muscle
30	chr19:40851000-40853600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:40851000-40853600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr19:40851000-40853600	Weak transcription	Right Atrium	heart
33	chr19:40851000-40853600	Weak transcription	Right Ventricle	heart
34	chr19:40852600-40853400	Enhancers	Placenta	Placenta
35	chr19:40852600-40853400	Enhancers	Gastric	stomach
36	chr19:40852600-40853600	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr19:40852600-40853600	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr19:40852800-40853400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr19:40852800-40853400	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr19:40852800-40853400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr19:40852800-40853400	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr19:40852800-40853400	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr19:40852800-40853400	Enhancers	Primary T cells from cord blood	blood
44	chr19:40852800-40853400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:40852800-40853400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr19:40852800-40853400	Enhancers	Adipose Nuclei	Adipose
47	chr19:40852800-40853400	Enhancers	Brain Cingulate Gyrus	brain
48	chr19:40852800-40853400	Enhancers	Brain Germinal Matrix	brain
49	chr19:40852800-40853400	Enhancers	Brain Substantia Nigra	brain
50	chr19:40852800-40853400	Enhancers	Duodenum Mucosa	Duodenum

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