Variant report

Variant	rs754255
Chromosome Location	chr19:19578890-19578891
allele	A/G
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:6)
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	KAP1	chr19:19578795-19579787	HEK293	kidney:	n/a	n/a
2	KAP1	chr19:19578645-19579928	K562	blood:	n/a	n/a
3	SETDB1	chr19:19578773-19579819	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19516490..19519551-chr19:19577584..19579824,3	MCF-7	breast:
2	chr19:19577936..19580342-chr19:19585609..19587741,3	MCF-7	breast:
3	chr19:19570376..19575066-chr19:19577857..19582377,6	K562	blood:
4	chr19:19571463..19575965-chr19:19576361..19580794,6	K562	blood:
5	chr19:19578231..19580851-chr19:19582569..19585456,2	K562	blood:
6	chr19:19515118..19519487-chr19:19577388..19580917,4	K562	blood:

No data

Variant related genes	Relation type
GATAD2A	TF binding region
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1000237	0.84[ASN][1000 genomes]
rs10282	0.81[ASN][1000 genomes]
rs10401193	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10402308	0.83[EUR][1000 genomes]
rs10402451	0.87[ASN][1000 genomes]
rs10402627	0.85[ASN][1000 genomes]
rs10404728	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10405625	0.91[ASN][1000 genomes]
rs10410664	0.91[ASN][1000 genomes]
rs10414830	0.91[ASN][1000 genomes]
rs10419912	0.86[ASN][1000 genomes]
rs10422819	0.81[ASN][1000 genomes]
rs1047361	0.87[ASN][1000 genomes]
rs1054284	0.93[ASN][1000 genomes]
rs1054930	0.81[ASN][1000 genomes]
rs1063966	0.85[ASN][1000 genomes]
rs11669516	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12972397	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12973258	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12975119	0.91[ASN][1000 genomes]
rs12977524	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12981405	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12983940	0.91[AMR][1000 genomes]
rs1465695	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1469712	0.91[ASN][1000 genomes]
rs1469713	0.90[ASN][1000 genomes]
rs17288409	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1808653	0.87[ASN][1000 genomes]
rs1858999	0.82[ASN][1000 genomes]
rs1865034	0.87[ASN][1000 genomes]
rs2082421	0.95[ASN][1000 genomes]
rs2099333	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2099334	0.91[ASN][1000 genomes]
rs2163804	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163805	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288852	0.87[ASN][1000 genomes]
rs2304098	0.81[ASN][1000 genomes]
rs2315279	0.81[ASN][1000 genomes]
rs2315610	0.86[ASN][1000 genomes]
rs28478453	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905431	0.81[ASN][1000 genomes]
rs2916069	0.84[ASN][1000 genomes]
rs2916073	0.91[ASN][1000 genomes]
rs2916074	0.91[ASN][1000 genomes]
rs2916076	0.91[ASN][1000 genomes]
rs2965180	0.82[ASN][1000 genomes]
rs2965182	0.91[ASN][1000 genomes]
rs2965183	0.91[ASN][1000 genomes]
rs2965188	0.85[ASN][1000 genomes]
rs2965189	0.84[ASN][1000 genomes]
rs34277109	0.82[ASN][1000 genomes]
rs34647936	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35418933	0.80[ASN][1000 genomes]
rs3752151	0.93[ASN][1000 genomes]
rs3794990	0.87[ASN][1000 genomes]
rs3794993	0.87[ASN][1000 genomes]
rs4808196	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4808198	0.90[ASN][1000 genomes]
rs4808199	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808200	0.91[ASN][1000 genomes]
rs4808202	0.91[ASN][1000 genomes]
rs4808203	0.91[ASN][1000 genomes]
rs4808950	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4808955	0.90[ASN][1000 genomes]
rs4808957	0.91[ASN][1000 genomes]
rs4808959	0.91[ASN][1000 genomes]
rs4808960	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808961	0.91[ASN][1000 genomes]
rs4808964	0.95[ASN][1000 genomes]
rs4808965	0.82[ASN][1000 genomes]
rs4808967	0.82[ASN][1000 genomes]
rs60003758	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60321073	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6511036	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511038	0.85[ASN][1000 genomes]
rs6909	0.85[ASN][1000 genomes]
rs7250658	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7250893	0.84[ASN][1000 genomes]
rs7252888	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7253807	0.82[ASN][1000 genomes]
rs7256149	0.93[ASN][1000 genomes]
rs7258508	0.81[EUR][1000 genomes]
rs747050	0.86[ASN][1000 genomes]
rs751856	0.87[ASN][1000 genomes]
rs751858	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs892021	0.87[ASN][1000 genomes]
rs892022	0.95[ASN][1000 genomes]
rs9917108	0.90[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs754255	KIAA0892	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19575600-19581600	ZNF genes & repeats	GM12878-XiMat	blood
2	chr19:19575800-19579000	Strong transcription	Rectal Mucosa Donor 31	rectum
3	chr19:19575800-19579600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr19:19575800-19579800	ZNF genes & repeats	Dnd41	blood
5	chr19:19575800-19580000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr19:19575800-19580600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
7	chr19:19575800-19580800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:19575800-19581600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:19576000-19579200	Strong transcription	Stomach Smooth Muscle	stomach
10	chr19:19576000-19579800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:19576200-19579600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:19576200-19580000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:19576200-19580200	ZNF genes & repeats	Thymus	Thymus
14	chr19:19576200-19580600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:19576200-19580800	ZNF genes & repeats	Primary B cells from cord blood	blood
16	chr19:19576400-19579200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
17	chr19:19576400-19580000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:19576400-19580600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr19:19576400-19580600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
20	chr19:19576400-19580600	ZNF genes & repeats	Fetal Thymus	thymus
21	chr19:19576600-19579000	Strong transcription	Placenta Amnion	Placenta Amnion
22	chr19:19576600-19580600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:19576600-19580800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr19:19576800-19579000	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr19:19576800-19579400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr19:19576800-19579800	ZNF genes & repeats	K562	blood
27	chr19:19576800-19579800	ZNF genes & repeats	NHDF-Ad	bronchial
28	chr19:19576800-19580800	ZNF genes & repeats	Fetal Intestine Small	intestine
29	chr19:19577000-19579400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
30	chr19:19577000-19579800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
31	chr19:19577000-19579800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
32	chr19:19577000-19580000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr19:19577000-19580400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
34	chr19:19577200-19580200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:19577200-19580200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
36	chr19:19577200-19580200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr19:19577200-19580600	ZNF genes & repeats	Fetal Stomach	stomach
38	chr19:19577400-19579800	ZNF genes & repeats	Primary T cells from cord blood	blood
39	chr19:19577400-19579800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:19577400-19579800	ZNF genes & repeats	Brain Germinal Matrix	brain
41	chr19:19577400-19580400	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr19:19577400-19580600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
43	chr19:19577600-19579400	ZNF genes & repeats	NHEK	skin
44	chr19:19577600-19579800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
45	chr19:19577600-19579800	ZNF genes & repeats	Brain Hippocampus Middle	brain
46	chr19:19577600-19579800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
47	chr19:19577600-19579800	ZNF genes & repeats	A549	lung
48	chr19:19577600-19579800	ZNF genes & repeats	HMEC	breast
49	chr19:19577600-19579800	ZNF genes & repeats	NHLF	lung
50	chr19:19577600-19580000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood

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