Variant report

Variant	rs2099333
Chromosome Location	chr19:19605963-19605964
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19604245..19607046-chr19:19609002..19611869,2	K562	blood:
2	chr19:19600750..19602890-chr19:19604803..19607283,5	K562	blood:
3	chr19:19604449..19607288-chr19:19625102..19626994,2	K562	blood:
4	chr19:19603656..19606213-chr19:19607284..19608859,2	K562	blood:
5	chr19:19605020..19607396-chr19:19612353..19614369,2	MCF-7	breast:
6	chr19:19605105..19607079-chr19:19610893..19613873,2	MCF-7	breast:
7	chr19:19602973..19607408-chr19:19609370..19612569,7	K562	blood:
8	chr19:19599544..19602338-chr19:19603143..19607030,3	K562	blood:
9	chr19:19600810..19602736-chr19:19605052..19607222,2	MCF-7	breast:
10	chr19:19604081..19605986-chr19:19620556..19622809,2	MCF-7	breast:
11	chr19:19604868..19608333-chr19:19608570..19610534,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000186010	Chromatin interaction
ENSG00000178093	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10282	0.86[ASN][1000 genomes]
rs10401193	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10402308	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10402451	0.91[ASN][1000 genomes]
rs10402627	0.90[ASN][1000 genomes]
rs10404728	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405625	0.87[ASN][1000 genomes]
rs10410664	0.87[ASN][1000 genomes]
rs10414830	0.87[ASN][1000 genomes]
rs10419912	0.90[ASN][1000 genomes]
rs10422819	0.86[ASN][1000 genomes]
rs1047361	0.91[ASN][1000 genomes]
rs1054284	0.98[ASN][1000 genomes]
rs1054930	0.86[ASN][1000 genomes]
rs1063966	0.90[ASN][1000 genomes]
rs11669516	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12972397	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12973258	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12975119	0.87[ASN][1000 genomes]
rs12977524	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12981405	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1465695	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1469712	0.87[ASN][1000 genomes]
rs1469713	0.85[ASN][1000 genomes]
rs17288409	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1808653	0.83[ASN][1000 genomes]
rs1865034	0.91[ASN][1000 genomes]
rs2082421	1.00[ASN][1000 genomes]
rs2099334	0.87[ASN][1000 genomes]
rs2163804	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2163805	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288852	0.91[ASN][1000 genomes]
rs2304098	0.86[ASN][1000 genomes]
rs2315610	0.91[ASN][1000 genomes]
rs28478453	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2916073	0.87[ASN][1000 genomes]
rs2916074	0.87[ASN][1000 genomes]
rs2916076	0.87[ASN][1000 genomes]
rs2965182	0.87[ASN][1000 genomes]
rs2965183	0.87[ASN][1000 genomes]
rs2965188	0.81[ASN][1000 genomes]
rs34647936	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3752151	0.98[ASN][1000 genomes]
rs3794990	0.91[ASN][1000 genomes]
rs3794993	0.91[ASN][1000 genomes]
rs4808196	0.84[EUR][1000 genomes]
rs4808198	0.85[ASN][1000 genomes]
rs4808199	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808200	0.87[ASN][1000 genomes]
rs4808202	0.87[ASN][1000 genomes]
rs4808203	0.87[ASN][1000 genomes]
rs4808208	0.84[ASN][1000 genomes]
rs4808950	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4808955	0.86[ASN][1000 genomes]
rs4808957	0.86[ASN][1000 genomes]
rs4808959	0.86[ASN][1000 genomes]
rs4808960	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808961	0.87[ASN][1000 genomes]
rs4808964	1.00[ASN][1000 genomes]
rs4808965	0.87[ASN][1000 genomes]
rs4808967	0.87[ASN][1000 genomes]
rs57009615	0.86[AFR][1000 genomes]
rs60003758	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60321073	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6511036	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6511038	0.90[ASN][1000 genomes]
rs6909	0.90[ASN][1000 genomes]
rs7245983	0.82[ASN][1000 genomes]
rs7250658	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7250893	0.88[ASN][1000 genomes]
rs7252888	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7253807	0.87[ASN][1000 genomes]
rs7256149	0.88[ASN][1000 genomes]
rs7258508	0.81[EUR][1000 genomes]
rs747050	0.91[ASN][1000 genomes]
rs751856	0.91[ASN][1000 genomes]
rs751858	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs754255	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs892021	0.91[ASN][1000 genomes]
rs892022	1.00[ASN][1000 genomes]
rs9917108	0.85[ASN][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	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
2	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2099333	KIAA0892	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19599000-19618000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:19600800-19619400	Strong transcription	Dnd41	blood
3	chr19:19601000-19606800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr19:19601000-19624600	Weak transcription	Fetal Brain Male	brain
5	chr19:19601200-19624800	Weak transcription	Fetal Kidney	kidney
6	chr19:19601200-19624800	Weak transcription	Right Atrium	heart
7	chr19:19601400-19609200	Weak transcription	Psoas Muscle	Psoas
8	chr19:19601400-19611800	Strong transcription	K562	blood
9	chr19:19601400-19612200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr19:19601400-19615200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:19601400-19619400	Strong transcription	Fetal Intestine Small	intestine
12	chr19:19601400-19624800	Weak transcription	Fetal Heart	heart
13	chr19:19601600-19606600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr19:19601600-19607400	Strong transcription	A549	lung
15	chr19:19601600-19608200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:19601600-19613400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr19:19601600-19619200	Strong transcription	Fetal Thymus	thymus
18	chr19:19601600-19619400	Strong transcription	Primary T cells from cord blood	blood
19	chr19:19601600-19619400	Strong transcription	Duodenum Mucosa	Duodenum
20	chr19:19601600-19619400	Strong transcription	Thymus	Thymus
21	chr19:19601600-19620000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr19:19601800-19606600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:19601800-19613800	Strong transcription	NHEK	skin
24	chr19:19601800-19616200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr19:19601800-19618000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
26	chr19:19601800-19618200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr19:19601800-19618400	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr19:19601800-19618800	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr19:19601800-19618800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr19:19601800-19619200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr19:19601800-19619200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr19:19601800-19619200	Strong transcription	Fetal Intestine Large	intestine
33	chr19:19601800-19619200	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr19:19601800-19619200	Strong transcription	Spleen	Spleen
35	chr19:19601800-19619400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr19:19601800-19619400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:19601800-19619400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr19:19601800-19619400	Strong transcription	NHLF	lung
39	chr19:19601800-19619600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr19:19601800-19619800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr19:19601800-19620400	Strong transcription	Fetal Stomach	stomach
42	chr19:19602000-19617800	Strong transcription	HepG2	liver
43	chr19:19602000-19618800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr19:19602000-19619000	Strong transcription	Placenta	Placenta
45	chr19:19602000-19619400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr19:19602000-19619400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:19602000-19619400	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr19:19602000-19619400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:19602000-19619800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:19602200-19614000	Strong transcription	Stomach Smooth Muscle	stomach

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