Variant report

Variant	rs10404728
Chromosome Location	chr19:19595014-19595015
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19573288..19575099-chr19:19594629..19597608,2	MCF-7	breast:
2	chr19:19591413..19595730-chr19:19599673..19603116,5	K562	blood:
3	chr19:19584133..19587197-chr19:19592002..19595372,3	K562	blood:
4	chr19:19515306..19517570-chr19:19594692..19597580,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10282	0.86[ASN][1000 genomes]
rs10401193	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10402308	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10402451	0.91[ASN][1000 genomes]
rs10402627	0.90[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	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12972397	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12973258	0.85[ASN][1000 genomes]
rs12975119	0.87[ASN][1000 genomes]
rs12977524	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12981405	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1465695	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1469712	0.87[ASN][1000 genomes]
rs1469713	0.85[ASN][1000 genomes]
rs17288409	0.88[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]
rs2099333	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099334	0.87[ASN][1000 genomes]
rs2163804	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2163805	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[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];0.84[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	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[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	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[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	0.81[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	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[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]
rs60003758	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60321073	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6511036	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[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	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7250893	0.88[ASN][1000 genomes]
rs7252888	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[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	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs754255	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[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
rs10404728	KIAA0892	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19577800-19598000	Weak transcription	Ovary	ovary
2	chr19:19579200-19598000	Weak transcription	Small Intestine	intestine
3	chr19:19579400-19599400	Weak transcription	Brain Angular Gyrus	brain
4	chr19:19579800-19595600	Weak transcription	Osteobl	bone
5	chr19:19579800-19595800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr19:19579800-19595800	Weak transcription	Colon Smooth Muscle	Colon
7	chr19:19579800-19595800	Weak transcription	HUVEC	blood vessel
8	chr19:19579800-19598600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr19:19579800-19599200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr19:19579800-19599800	Weak transcription	Brain Substantia Nigra	brain
11	chr19:19580600-19595200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr19:19580600-19597200	Weak transcription	Brain Anterior Caudate	brain
13	chr19:19581600-19595200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:19582200-19597600	Strong transcription	Dnd41	blood
15	chr19:19584200-19600000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr19:19584400-19595600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:19585400-19596000	Weak transcription	HMEC	breast
18	chr19:19586400-19595600	Weak transcription	NHDF-Ad	bronchial
19	chr19:19587000-19595600	Weak transcription	Left Ventricle	heart
20	chr19:19587000-19599000	Weak transcription	Brain Germinal Matrix	brain
21	chr19:19587000-19599200	Weak transcription	Fetal Brain Female	brain
22	chr19:19587200-19599600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr19:19587400-19595600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr19:19587600-19595200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr19:19587600-19598600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr19:19588000-19598400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr19:19588800-19597200	Weak transcription	Pancreas	Pancrea
28	chr19:19588800-19597800	Weak transcription	Colonic Mucosa	Colon
29	chr19:19588800-19597800	Weak transcription	A549	lung
30	chr19:19588800-19599200	Weak transcription	Hela-S3	cervix
31	chr19:19589200-19597600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr19:19589200-19598000	Weak transcription	Esophagus	oesophagus
33	chr19:19589400-19598400	Weak transcription	Stomach Mucosa	stomach
34	chr19:19590400-19597400	Strong transcription	Duodenum Mucosa	Duodenum
35	chr19:19590400-19597800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr19:19590400-19599400	Genic enhancers	Fetal Thymus	thymus
37	chr19:19590600-19595200	Genic enhancers	Primary T cells fromperipheralblood	blood
38	chr19:19590800-19598000	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr19:19591000-19596000	Weak transcription	K562	blood
40	chr19:19591200-19595800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr19:19591200-19598000	Genic enhancers	Fetal Muscle Leg	muscle
42	chr19:19591400-19598600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr19:19591400-19598800	Genic enhancers	Fetal Muscle Trunk	muscle
44	chr19:19591600-19595400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr19:19591600-19595800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr19:19591600-19596600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr19:19591800-19595800	Weak transcription	Brain Hippocampus Middle	brain
48	chr19:19592000-19599200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr19:19592200-19595600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:19592200-19595600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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