Variant report

Variant	rs2999278
Chromosome Location	chr10:44053585-44053586
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:44048373..44055141-chr10:44068006..44071269,9	K562	blood:
2	chr10:44052358..44053877-chr10:44114042..44116441,2	K562	blood:
3	chr10:44047431..44049716-chr10:44053122..44055103,2	K562	blood:
4	chr10:44051533..44053813-chr10:44055767..44057856,2	K562	blood:
5	chr10:44053072..44054860-chr10:44068612..44070117,2	K562	blood:
6	chr10:44053306..44056176-chr10:44066211..44067733,2	K562	blood:
7	chr10:44045670..44047822-chr10:44049700..44053652,4	K562	blood:

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

Chromatin state (count:99 , 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	chr10:44049400-44055800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
3	chr10:44049600-44055400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr10:44050000-44055400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
5	chr10:44050000-44057800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr10:44050000-44058600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr10:44050200-44054200	Strong transcription	Skeletal Muscle Female	skeletal muscle
8	chr10:44050200-44055000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
9	chr10:44050200-44055000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr10:44050200-44055000	ZNF genes & repeats	Aorta	Aorta
11	chr10:44050400-44053800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
12	chr10:44050400-44069200	Weak transcription	Fetal Thymus	thymus
13	chr10:44050600-44053600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr10:44050600-44055000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr10:44050600-44055400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
16	chr10:44050600-44055600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr10:44050600-44056000	ZNF genes & repeats	Liver	Liver
18	chr10:44050600-44056200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
19	chr10:44050600-44056400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr10:44050800-44053600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
21	chr10:44050800-44053600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
22	chr10:44050800-44053600	ZNF genes & repeats	Ovary	ovary
23	chr10:44050800-44053800	Strong transcription	Brain Angular Gyrus	brain
24	chr10:44050800-44055000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
25	chr10:44050800-44055000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr10:44050800-44055600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr10:44050800-44056000	ZNF genes & repeats	K562	blood
28	chr10:44050800-44056800	ZNF genes & repeats	Primary T cells from cord blood	blood
29	chr10:44051000-44055000	ZNF genes & repeats	Fetal Muscle Leg	muscle
30	chr10:44051200-44053600	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr10:44051200-44054000	ZNF genes & repeats	Primary B cells from cord blood	blood
32	chr10:44051200-44054200	ZNF genes & repeats	Fetal Stomach	stomach
33	chr10:44051200-44054400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
34	chr10:44051200-44055000	ZNF genes & repeats	Fetal Intestine Small	intestine
35	chr10:44051200-44056800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr10:44051400-44053800	Weak transcription	Fetal Heart	heart
37	chr10:44051400-44053800	ZNF genes & repeats	Small Intestine	intestine
38	chr10:44051400-44054000	Strong transcription	Fetal Brain Male	brain
39	chr10:44051400-44055200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
40	chr10:44051400-44055400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
41	chr10:44051600-44053600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
42	chr10:44051600-44054200	Strong transcription	Brain Anterior Caudate	brain
43	chr10:44051800-44054200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr10:44051800-44055600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
45	chr10:44052000-44053600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr10:44052000-44053600	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr10:44052000-44053600	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr10:44052000-44053600	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr10:44052000-44053600	ZNF genes & repeats	NH-A	brain
50	chr10:44052000-44053800	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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