Variant report

Variant	rs6511036
Chromosome Location	chr19:19582651-19582652
allele	A/G
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	EBF1	chr19:19582475-19582786	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:19582575-19582809	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:19582521-19582844	K562	blood:	n/a	n/a
4	RUNX3	chr19:19582265-19582772	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:19582623-19582812	K562	blood:	n/a	n/a
6	RUNX3	chr19:19582094-19582952	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19573739..19577960-chr19:19580596..19583736,3	MCF-7	breast:
2	chr19:19574470..19576025-chr19:19580861..19583746,2	MCF-7	breast:
3	chr19:19580831..19583054-chr19:19584529..19587065,3	K562	blood:

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

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1000237	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1009136	0.80[JPT][hapmap]
rs1010207	0.81[JPT][hapmap]
rs10282	0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10401193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10402308	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[EUR][1000 genomes]
rs10402451	0.88[ASN][1000 genomes]
rs10402627	0.87[ASN][1000 genomes]
rs10404728	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10405625	0.90[ASN][1000 genomes]
rs10410664	0.90[ASN][1000 genomes]
rs10414830	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs10419912	0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs10422819	0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1047361	0.88[ASN][1000 genomes]
rs1054284	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1054930	0.83[ASN][1000 genomes]
rs1063966	0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs11085259	0.94[CEU][hapmap]
rs11669516	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12972397	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12973258	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12975119	0.90[ASN][1000 genomes]
rs12977524	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12981405	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1465695	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1469712	0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1469713	0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs16996148	0.93[YRI][hapmap]
rs17288409	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1808653	0.86[ASN][1000 genomes]
rs1858999	0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1859287	0.93[CEU][hapmap];0.84[JPT][hapmap]
rs1865034	0.88[ASN][1000 genomes]
rs2023883	0.93[CEU][hapmap];0.84[JPT][hapmap]
rs2082421	0.97[ASN][1000 genomes]
rs2099333	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2099334	0.90[ASN][1000 genomes]
rs2163804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2163805	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2285628	1.00[CEU][hapmap]
rs2288852	0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2301668	0.93[CEU][hapmap]
rs2301786	0.81[JPT][hapmap]
rs2304098	0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2315025	0.81[JPT][hapmap]
rs2315610	0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs28478453	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2905424	0.80[JPT][hapmap]
rs2905425	0.81[JPT][hapmap]
rs2916069	0.82[ASN][1000 genomes]
rs2916073	0.90[ASN][1000 genomes]
rs2916074	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2916076	0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2965180	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2965182	0.90[ASN][1000 genomes]
rs2965183	0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2965188	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2965189	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2965198	0.81[JPT][hapmap]
rs34277109	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs34647936	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3752151	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3764567	0.84[JPT][hapmap]
rs3794990	0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3794993	0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs4808194	0.94[CEU][hapmap]
rs4808196	0.82[EUR][1000 genomes]
rs4808198	0.88[ASN][1000 genomes]
rs4808199	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808200	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4808202	0.90[ASN][1000 genomes]
rs4808203	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4808208	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4808950	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808955	0.89[ASN][1000 genomes]
rs4808957	0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4808959	0.94[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs4808960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808961	0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs4808964	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4808965	0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4808967	0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs57009615	0.81[AFR][1000 genomes]
rs60003758	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60321073	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6511038	0.87[ASN][1000 genomes]
rs6909	0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs7245983	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs7250658	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7250893	0.85[ASN][1000 genomes]
rs7252888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7253807	0.84[ASN][1000 genomes]
rs7254230	0.81[JPT][hapmap]
rs7256149	0.91[ASN][1000 genomes]
rs7259434	0.94[CEU][hapmap];0.85[JPT][hapmap]
rs747050	0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs751856	0.88[ASN][1000 genomes]
rs751858	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs754255	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8108647	0.93[CEU][hapmap]
rs892021	0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs892022	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs968525	0.93[CEU][hapmap]
rs9917108	0.88[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
rs6511036	KIAA0892	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19577800-19598000	Weak transcription	Ovary	ovary
2	chr19:19578000-19583600	Weak transcription	Pancreas	Pancrea
3	chr19:19579000-19584800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:19579200-19583400	Weak transcription	Esophagus	oesophagus
5	chr19:19579200-19583400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr19:19579200-19583800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:19579200-19585000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr19:19579200-19585000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:19579200-19585400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr19:19579200-19585800	Weak transcription	Hela-S3	cervix
11	chr19:19579200-19586000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:19579200-19598000	Weak transcription	Small Intestine	intestine
13	chr19:19579400-19584000	Weak transcription	Right Ventricle	heart
14	chr19:19579400-19585600	Weak transcription	Fetal Heart	heart
15	chr19:19579400-19599400	Weak transcription	Brain Angular Gyrus	brain
16	chr19:19579600-19583600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr19:19579600-19584800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:19579800-19582800	Weak transcription	HSMMtube	muscle
19	chr19:19579800-19583200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:19579800-19583400	Weak transcription	Colonic Mucosa	Colon
21	chr19:19579800-19583400	Weak transcription	A549	lung
22	chr19:19579800-19583600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:19579800-19583600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:19579800-19583600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr19:19579800-19583600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr19:19579800-19583600	Weak transcription	HMEC	breast
27	chr19:19579800-19583600	Weak transcription	NHLF	lung
28	chr19:19579800-19583800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr19:19579800-19583800	Weak transcription	Brain Hippocampus Middle	brain
30	chr19:19579800-19583800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr19:19579800-19583800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr19:19579800-19585000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr19:19579800-19585000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr19:19579800-19585000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr19:19579800-19585200	Weak transcription	Brain Germinal Matrix	brain
36	chr19:19579800-19585400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr19:19579800-19585400	Weak transcription	NHDF-Ad	bronchial
38	chr19:19579800-19585600	Weak transcription	Fetal Brain Female	brain
39	chr19:19579800-19587400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr19:19579800-19591000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr19:19579800-19593400	Weak transcription	Fetal Kidney	kidney
42	chr19:19579800-19595600	Weak transcription	Osteobl	bone
43	chr19:19579800-19595800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr19:19579800-19595800	Weak transcription	Colon Smooth Muscle	Colon
45	chr19:19579800-19595800	Weak transcription	HUVEC	blood vessel
46	chr19:19579800-19598600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:19579800-19599200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr19:19579800-19599800	Weak transcription	Brain Substantia Nigra	brain
49	chr19:19580000-19583400	Weak transcription	Fetal Muscle Trunk	muscle
50	chr19:19580000-19583800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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