Variant report

Variant	rs2999280
Chromosome Location	chr10:44056242-44056243
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:44053796..44056981-chr10:44062338..44065118,5	MCF-7	breast:
2	chr10:44039393..44042249-chr10:44054829..44056405,2	K562	blood:
3	chr10:44051533..44053813-chr10:44055767..44057856,2	K562	blood:
4	chr10:44055755..44058287-chr10:44068449..44071226,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196793	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	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10793443	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10899827	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]
rs10899828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11238585	0.94[ASN][1000 genomes]
rs11238588	0.82[CHB][hapmap];0.96[ASN][1000 genomes]
rs12354445	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12415781	0.84[ASN][1000 genomes]
rs12784891	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1338565	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1832470	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2230660	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2230661	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2393938	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2393939	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2393942	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2393959	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2393960	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2860340	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999270	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2999271	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999272	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999273	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2999274	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999277	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999278	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999279	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3006379	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3006380	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3006383	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3006384	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3006385	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3763789	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4948747	0.90[ASN][1000 genomes]
rs6593359	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7078691	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7079328	0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7086537	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7089577	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7091995	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7092156	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7101356	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7893169	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7894102	0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7897611	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7906129	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7913084	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7915227	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9326506	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9422385	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9422388	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9422540	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9422541	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9422543	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9422544	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9422545	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9422546	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9422547	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9422549	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9422550	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9422555	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9422557	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[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
rs2999280	ZNF239	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44049000-44057200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
2	chr10:44050000-44057800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:44050000-44058600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
4	chr10:44050400-44069200	Weak transcription	Fetal Thymus	thymus
5	chr10:44050600-44056400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr10:44050800-44056800	ZNF genes & repeats	Primary T cells from cord blood	blood
7	chr10:44051200-44056800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr10:44053000-44069000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr10:44053000-44069200	Weak transcription	Thymus	Thymus
10	chr10:44053200-44062600	Weak transcription	Brain Germinal Matrix	brain
11	chr10:44053200-44062800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr10:44053200-44066600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr10:44053200-44068400	Weak transcription	NHDF-Ad	bronchial
14	chr10:44053200-44068800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr10:44053200-44068800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr10:44053200-44068800	Weak transcription	Hela-S3	cervix
17	chr10:44053200-44068800	Weak transcription	HSMMtube	muscle
18	chr10:44053400-44062800	Weak transcription	Adipose Nuclei	Adipose
19	chr10:44053400-44068800	Weak transcription	Brain Substantia Nigra	brain
20	chr10:44053600-44057000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr10:44053600-44057800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr10:44053600-44058200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr10:44053600-44059200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr10:44053600-44059200	Weak transcription	Pancreas	Pancrea
25	chr10:44053600-44059200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr10:44053600-44061600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr10:44053600-44062600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr10:44053600-44062800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr10:44053600-44064400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr10:44053600-44064600	Weak transcription	NHLF	lung
31	chr10:44053600-44068200	Weak transcription	Fetal Kidney	kidney
32	chr10:44053600-44068600	Weak transcription	NH-A	brain
33	chr10:44053600-44068800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr10:44053600-44068800	Weak transcription	Psoas Muscle	Psoas
35	chr10:44053600-44068800	Weak transcription	Right Ventricle	heart
36	chr10:44053600-44069000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr10:44053600-44069200	Weak transcription	Left Ventricle	heart
38	chr10:44053800-44059200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr10:44053800-44061600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr10:44053800-44061600	Weak transcription	Fetal Brain Female	brain
41	chr10:44053800-44063200	Weak transcription	Brain Angular Gyrus	brain
42	chr10:44053800-44066600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr10:44053800-44068600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr10:44053800-44068800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr10:44053800-44069000	Weak transcription	HSMM	muscle
46	chr10:44054000-44057800	Weak transcription	Primary B cells from cord blood	blood
47	chr10:44054200-44057600	Weak transcription	Brain Anterior Caudate	brain
48	chr10:44054200-44058000	Weak transcription	Fetal Stomach	stomach
49	chr10:44054200-44061400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr10:44054200-44062800	Weak transcription	Rectal Smooth Muscle	rectum

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