Variant report

Variant	rs1534828
Chromosome Location	chr9:104168517-104168518
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:104165233..104170505-chr9:104171045..104175682,8	MCF-7	breast:
2	chr9:104167280..104171241-chr9:104178855..104183117,5	K562	blood:
3	chr9:104160803..104165206-chr9:104167116..104171399,6	K562	blood:
4	chr9:104167820..104171241-chr9:104178855..104183117,4	K562	blood:

Variant related genes	Relation type
ENSG00000136870	Chromatin interaction
ENSG00000136897	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1047968	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1047971	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10491511	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10512281	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10989500	1.00[CHD][hapmap];1.00[MKK][hapmap]
rs17185855	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17186534	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17186716	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17186905	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17186933	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17766676	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772272	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772308	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772331	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772355	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772514	1.00[CHD][hapmap];1.00[MKK][hapmap]
rs17772612	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772672	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772839	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772845	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772869	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17773040	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17773076	1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MKK][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1929488	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1929489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1929491	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1929492	1.00[MKK][hapmap]
rs2028031	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2734469	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41296049	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41308902	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs954738	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][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	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1534828	ZNF189	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104162000-104169600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:104162600-104170400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:104162600-104170400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:104162600-104171600	Strong transcription	Placenta	Placenta
5	chr9:104162600-104172000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:104162800-104169000	Strong transcription	HSMMtube	muscle
7	chr9:104162800-104169200	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:104162800-104169400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr9:104162800-104169600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:104162800-104170000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr9:104162800-104170000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:104162800-104172200	ZNF genes & repeats	A549	lung
13	chr9:104162800-104173800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr9:104163000-104169600	Strong transcription	Fetal Thymus	thymus
15	chr9:104163000-104169800	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr9:104163000-104173000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
17	chr9:104163200-104168600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr9:104163200-104169200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:104163200-104170200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr9:104163200-104172600	ZNF genes & repeats	Primary B cells from cord blood	blood
21	chr9:104163200-104174000	ZNF genes & repeats	Fetal Lung	lung
22	chr9:104163400-104168600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:104163400-104172200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr9:104163400-104174000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr9:104163600-104170600	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr9:104163600-104173600	ZNF genes & repeats	Ovary	ovary
27	chr9:104164000-104170000	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr9:104164000-104173600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:104164200-104172200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:104164400-104171800	ZNF genes & repeats	Dnd41	blood
31	chr9:104164400-104172000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr9:104164400-104173400	ZNF genes & repeats	Colon Smooth Muscle	Colon
33	chr9:104164600-104168600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr9:104164600-104173600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:104164600-104173800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr9:104164800-104173400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
37	chr9:104164800-104174200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr9:104164800-104174200	ZNF genes & repeats	Brain Hippocampus Middle	brain
39	chr9:104164800-104175400	ZNF genes & repeats	Fetal Muscle Leg	muscle
40	chr9:104165000-104169000	Strong transcription	Brain Angular Gyrus	brain
41	chr9:104165000-104173800	ZNF genes & repeats	Liver	Liver
42	chr9:104165200-104170200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
43	chr9:104165200-104172000	ZNF genes & repeats	Fetal Intestine Large	intestine
44	chr9:104165200-104172000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
45	chr9:104165200-104172200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
46	chr9:104165200-104172200	ZNF genes & repeats	GM12878-XiMat	blood
47	chr9:104165200-104172200	ZNF genes & repeats	K562	blood
48	chr9:104165200-104172600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
49	chr9:104165200-104172800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr9:104165400-104172000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland

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