Variant report

Variant	rs9422544
Chromosome Location	chr10:44069524-44069525
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:44063474..44065679-chr10:44068799..44071087,3	MCF-7	breast:
2	chr10:44051560..44053366-chr10:44067715..44069779,2	MCF-7	breast:
3	chr10:44068167..44069924-chr10:44136851..44139304,2	MCF-7	breast:
4	chr10:44060724..44063218-chr10:44066954..44069931,3	MCF-7	breast:
5	chr10:44068172..44069784-chr10:44100489..44103269,2	K562	blood:
6	chr10:44068620..44071892-chr10:44099602..44104778,6	MCF-7	breast:
7	chr10:43902074..43907022-chr10:44065945..44069589,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232004	Chromatin interaction
ENSG00000196793	Chromatin interaction
ENSG00000169813	Chromatin interaction
ENSG00000198298	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10793442	0.96[ASN][1000 genomes]
rs10793443	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899827	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899828	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11238585	0.94[ASN][1000 genomes]
rs11238588	0.97[ASN][1000 genomes]
rs12354445	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12415781	0.85[ASN][1000 genomes]
rs12784891	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1338565	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1832470	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2230660	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2230661	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2393938	0.98[ASN][1000 genomes]
rs2393939	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2393942	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2393959	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2393960	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2860340	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999270	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2999271	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999272	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999273	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2999274	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999277	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999278	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999279	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999280	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3006379	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3006380	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3006383	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3006384	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3006385	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3763789	0.98[ASN][1000 genomes]
rs4948747	0.95[ASN][1000 genomes]
rs6593359	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7078691	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7079328	0.94[ASN][1000 genomes]
rs7086537	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7089577	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7091995	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7092156	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7101356	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7893169	0.96[ASN][1000 genomes]
rs7894102	0.96[ASN][1000 genomes]
rs7897611	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7906129	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7913084	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7915227	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9326506	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9422385	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9422388	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9422540	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9422541	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9422543	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9422545	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9422546	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9422547	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9422549	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9422550	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9422555	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9422557	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];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	esv1798523	chr10:44051698-44070754	Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9422544	ZNF239	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44055000-44069600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr10:44055400-44070000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr10:44063600-44069600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr10:44068200-44070600	Active TSS	Fetal Kidney	kidney
5	chr10:44068400-44069600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr10:44068800-44069600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr10:44068800-44069600	ZNF genes & repeats	Primary B cells from cord blood	blood
8	chr10:44068800-44069600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr10:44068800-44069600	Flanking Active TSS	Hela-S3	cervix
10	chr10:44068800-44069800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr10:44068800-44069800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr10:44068800-44070600	Active TSS	NHLF	lung
13	chr10:44069000-44069600	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr10:44069000-44069600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr10:44069000-44069600	Enhancers	Primary B cells from peripheral blood	blood
16	chr10:44069000-44069600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr10:44069000-44069600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr10:44069000-44069600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr10:44069000-44069600	Active TSS	Liver	Liver
20	chr10:44069000-44069600	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr10:44069000-44069600	Flanking Active TSS	Fetal Muscle Leg	muscle
22	chr10:44069000-44069600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr10:44069000-44069600	Flanking Active TSS	HSMMtube	muscle
24	chr10:44069000-44069800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr10:44069000-44069800	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr10:44069000-44069800	Flanking Active TSS	Fetal Muscle Trunk	muscle
27	chr10:44069000-44070000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr10:44069000-44070200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr10:44069000-44070400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr10:44069000-44070400	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr10:44069000-44070400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr10:44069000-44070400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr10:44069000-44070400	Active TSS	Psoas Muscle	Psoas
34	chr10:44069000-44070400	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr10:44069000-44070600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
36	chr10:44069000-44070600	Active TSS	HSMM	muscle
37	chr10:44069000-44070800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
38	chr10:44069000-44070800	ZNF genes & repeats	GM12878-XiMat	blood
39	chr10:44069200-44069600	Enhancers	Primary T cells from cord blood	blood
40	chr10:44069200-44069600	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr10:44069200-44069600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
42	chr10:44069200-44069600	Flanking Active TSS	Left Ventricle	heart
43	chr10:44069200-44069600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
44	chr10:44069200-44069600	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr10:44069200-44069800	Active TSS	Colonic Mucosa	Colon
46	chr10:44069200-44069800	Flanking Active TSS	Fetal Thymus	thymus
47	chr10:44069200-44069800	Flanking Active TSS	Right Ventricle	heart
48	chr10:44069200-44070200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr10:44069200-44070200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
50	chr10:44069200-44070200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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