Variant report

Variant	rs10899827
Chromosome Location	chr10:44057364-44057365
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:44056427..44058289-chr10:44062144..44064267,2	K562	blood:
2	chr10:44051533..44053813-chr10:44055767..44057856,2	K562	blood:
3	chr10:44055755..44058287-chr10:44068449..44071226,4	MCF-7	breast:
4	chr10:44056360..44057931-chr10:44136986..44139717,2	K562	blood:

Variant related genes	Relation type
ENSG00000196793	Chromatin interaction
ENSG00000226245	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	0.95[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs10793443	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899828	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11238585	0.96[ASN][1000 genomes]
rs11238588	0.87[CHB][hapmap];0.81[JPT][hapmap];0.99[ASN][1000 genomes]
rs12354445	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12415781	0.87[ASN][1000 genomes]
rs12784891	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1338565	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1832470	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2230660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2230661	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2393938	0.95[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs2393939	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2393942	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2393959	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2393960	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2860340	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2999270	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999271	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2999272	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2999273	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2999274	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2999277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2999278	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2999279	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2999280	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3006379	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3006380	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3006383	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3006384	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3006385	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3763789	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4948747	0.93[ASN][1000 genomes]
rs6593359	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7078691	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7079328	0.90[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7086537	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7089577	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7091995	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7092156	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7101356	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7893169	0.95[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs7894102	0.90[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs7897611	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7906129	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7913084	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7915227	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9326506	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9422385	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9422388	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9422540	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9422541	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs9422543	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9422544	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9422545	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9422546	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9422547	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9422549	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9422550	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9422555	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9422557	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[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
rs10899827	ZNF239	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44050000-44057800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:44050000-44058600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
3	chr10:44050400-44069200	Weak transcription	Fetal Thymus	thymus
4	chr10:44053000-44069000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr10:44053000-44069200	Weak transcription	Thymus	Thymus
6	chr10:44053200-44062600	Weak transcription	Brain Germinal Matrix	brain
7	chr10:44053200-44062800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr10:44053200-44066600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr10:44053200-44068400	Weak transcription	NHDF-Ad	bronchial
10	chr10:44053200-44068800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr10:44053200-44068800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr10:44053200-44068800	Weak transcription	Hela-S3	cervix
13	chr10:44053200-44068800	Weak transcription	HSMMtube	muscle
14	chr10:44053400-44062800	Weak transcription	Adipose Nuclei	Adipose
15	chr10:44053400-44068800	Weak transcription	Brain Substantia Nigra	brain
16	chr10:44053600-44057800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr10:44053600-44058200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr10:44053600-44059200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr10:44053600-44059200	Weak transcription	Pancreas	Pancrea
20	chr10:44053600-44059200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr10:44053600-44061600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr10:44053600-44062600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr10:44053600-44062800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr10:44053600-44064400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr10:44053600-44064600	Weak transcription	NHLF	lung
26	chr10:44053600-44068200	Weak transcription	Fetal Kidney	kidney
27	chr10:44053600-44068600	Weak transcription	NH-A	brain
28	chr10:44053600-44068800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr10:44053600-44068800	Weak transcription	Psoas Muscle	Psoas
30	chr10:44053600-44068800	Weak transcription	Right Ventricle	heart
31	chr10:44053600-44069000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr10:44053600-44069200	Weak transcription	Left Ventricle	heart
33	chr10:44053800-44059200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr10:44053800-44061600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr10:44053800-44061600	Weak transcription	Fetal Brain Female	brain
36	chr10:44053800-44063200	Weak transcription	Brain Angular Gyrus	brain
37	chr10:44053800-44066600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr10:44053800-44068600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr10:44053800-44068800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr10:44053800-44069000	Weak transcription	HSMM	muscle
41	chr10:44054000-44057800	Weak transcription	Primary B cells from cord blood	blood
42	chr10:44054200-44057600	Weak transcription	Brain Anterior Caudate	brain
43	chr10:44054200-44058000	Weak transcription	Fetal Stomach	stomach
44	chr10:44054200-44061400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr10:44054200-44062800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr10:44054200-44069000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr10:44054400-44066400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr10:44055000-44057600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr10:44055000-44057600	Weak transcription	Fetal Lung	lung
50	chr10:44055000-44058000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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