Variant report

Variant	rs60839064
Chromosome Location	chr10:45491550-45491551
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr10:45491275-45491772	T-47D	breast:	n/a	n/a
2	NFIC	chr10:45491155-45492366	HepG2	liver:	n/a	n/a
3	JUND	chr10:45491263-45491728	HepG2	liver:	n/a	n/a
4	POLR2A	chr10:45491442-45492320	U87	brain:	n/a	n/a
5	FOXA1	chr10:45491265-45491707	T-47D	breast:	n/a	n/a
6	JUND	chr10:45491270-45491644	HepG2	liver:	n/a	n/a
7	FOXA1	chr10:45491241-45491714	T-47D	breast:	n/a	n/a
8	CEBPD	chr10:45491255-45491626	HepG2	liver:	n/a	n/a
9	POLR2A	chr10:45491166-45492604	HepG2	liver:	n/a	n/a
10	REST	chr10:45491239-45491773	HepG2	liver:	n/a	n/a
11	MAX	chr10:45491348-45492410	HUVEC	blood vessel:	n/a	chr10:45491936-45491947 chr10:45491642-45491651
12	ARID3A	chr10:45491249-45492276	HepG2	liver:	n/a	n/a
13	CEBPB	chr10:45491191-45491730	MCF-7	breast:	n/a	chr10:45491441-45491454
14	MXI1	chr10:45491260-45492341	HepG2	liver:	n/a	n/a
15	MBD4	chr10:45491227-45491669	HepG2	liver:	n/a	n/a
16	GATA3	chr10:45491237-45491808	T-47D	breast:	n/a	n/a
17	POLR2A	chr10:45491455-45492568	HL-60	blood:	n/a	n/a
18	NFIC	chr10:45491011-45492197	HepG2	liver:	n/a	n/a
19	TCF7L2	chr10:45491326-45491659	MCF-7	breast:	n/a	n/a
20	MAX	chr10:45491460-45492097	HepG2	liver:	n/a	chr10:45491936-45491947 chr10:45491642-45491651
21	RXRA	chr10:45491259-45492087	HepG2	liver:	n/a	chr10:45491972-45491991 chr10:45491983-45491999
22	HDAC2	chr10:45491279-45491704	HepG2	liver:	n/a	n/a
23	POLR2A	chr10:45491546-45492254	U87	brain:	n/a	n/a
24	FOXA1	chr10:45491209-45491826	HepG2	liver:	n/a	n/a
25	HEY1	chr10:45491180-45492421	HepG2	liver:	n/a	n/a
26	MAFF	chr10:45491281-45491614	HepG2	liver:	n/a	n/a
27	EP300	chr10:45491134-45492251	HepG2	liver:	n/a	n/a
28	MAX	chr10:45491087-45492506	HepG2	liver:	n/a	chr10:45491936-45491947 chr10:45491642-45491651
29	CEBPB	chr10:45491238-45491655	HepG2	liver:	n/a	chr10:45491441-45491454
30	HNF4A	chr10:45491344-45491694	HepG2	liver:	n/a	n/a
31	CEBPB	chr10:45491195-45491716	MCF-7	breast:	n/a	chr10:45491441-45491454
32	MBD4	chr10:45491089-45492207	HepG2	liver:	n/a	n/a
33	MYBL2	chr10:45491106-45492292	HepG2	liver:	n/a	n/a
34	POLR2A	chr10:45490763-45493058	HepG2	liver:	n/a	n/a
35	JUND	chr10:45491347-45491656	HepG2	liver:	n/a	n/a
36	POLR2A	chr10:45491199-45493109	HUVEC	blood vessel:	n/a	n/a
37	FOSL2	chr10:45491239-45492430	HepG2	liver:	n/a	chr10:45492170-45492181
38	CEBPB	chr10:45491243-45491607	HepG2	liver:	n/a	chr10:45491441-45491454
39	STAT3	chr10:45491405-45491659	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr10:45491508-45492368	HL-60	blood:	n/a	n/a
41	POLR2A	chr10:45491418-45491790	MCF10A-Er-Src	breast:	n/a	n/a
42	SP1	chr10:45491159-45492361	HepG2	liver:	n/a	n/a
43	EP300	chr10:45491164-45491843	HepG2	liver:	n/a	n/a
44	POLR2A	chr10:45491247-45492342	HUVEC	blood vessel:	n/a	n/a
45	FOXA1	chr10:45491119-45492019	HepG2	liver:	n/a	n/a
46	TCF7L2	chr10:45491259-45491694	HepG2	liver:	n/a	n/a
47	FOXA1	chr10:45491200-45492302	HepG2	liver:	n/a	n/a
48	POLR2A	chr10:45491496-45492381	HepG2	liver:	n/a	n/a
49	RFX5	chr10:45491400-45492172	HepG2	liver:	n/a	n/a
50	POLR2A	chr10:45489983-45493423	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:45428885..45431662-chr10:45490818..45493446,2	K562	blood:

Variant related genes	Relation type
ZNF22	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs57644166	1.00[AMR][1000 genomes]
rs58139903	1.00[AMR][1000 genomes]
rs58684533	1.00[AMR][1000 genomes]
rs60575180	1.00[AMR][1000 genomes]
rs73279386	1.00[AMR][1000 genomes]
rs73281403	1.00[AMR][1000 genomes]
rs73281405	1.00[AMR][1000 genomes]
rs73283447	1.00[AMR][1000 genomes]
rs73283451	1.00[AMR][1000 genomes]
rs73283455	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73283462	1.00[AMR][1000 genomes]
rs73283464	1.00[AMR][1000 genomes]
rs73283470	1.00[AMR][1000 genomes]
rs73285555	1.00[AMR][1000 genomes]
rs73285558	1.00[AMR][1000 genomes]
rs73287510	1.00[AMR][1000 genomes]
rs73287546	1.00[AMR][1000 genomes]
rs73287549	1.00[AMR][1000 genomes]
rs73287556	1.00[AMR][1000 genomes]
rs73287562	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv526734	chr10:45458485-45492054	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv831848	chr10:45490176-45667670	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45478800-45495800	Weak transcription	HMEC	breast
2	chr10:45482400-45495600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:45484200-45494200	Enhancers	Right Atrium	heart
4	chr10:45484600-45494200	Enhancers	Ovary	ovary
5	chr10:45485200-45493600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr10:45486000-45495600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr10:45486000-45495600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr10:45487200-45495600	Weak transcription	Brain Germinal Matrix	brain
9	chr10:45487200-45496200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:45487400-45495600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr10:45487800-45495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr10:45488200-45492000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr10:45488200-45492000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr10:45488200-45496000	Enhancers	Placenta	Placenta
15	chr10:45488400-45495800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr10:45488800-45491800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr10:45488800-45492600	Enhancers	Gastric	stomach
18	chr10:45488800-45492800	Enhancers	NHLF	lung
19	chr10:45488800-45493000	Enhancers	Esophagus	oesophagus
20	chr10:45488800-45495600	Enhancers	Primary hematopoietic stem cells	blood
21	chr10:45489000-45492000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr10:45489000-45492800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr10:45489000-45493200	Enhancers	NHDF-Ad	bronchial
24	chr10:45489200-45492400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr10:45489200-45492600	Enhancers	Muscle Satellite Cultured Cells	--
26	chr10:45489200-45493600	Enhancers	HUVEC	blood vessel
27	chr10:45489200-45494200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr10:45489200-45494200	Enhancers	Lung	lung
29	chr10:45489200-45495200	Enhancers	Dnd41	blood
30	chr10:45489200-45495600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr10:45489400-45491600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr10:45489400-45492200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr10:45489400-45492200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr10:45489400-45495200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr10:45489400-45495400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr10:45489600-45491600	Weak transcription	Fetal Intestine Large	intestine
37	chr10:45489600-45491600	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr10:45489600-45491600	Enhancers	HepG2	liver
39	chr10:45489600-45491800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr10:45489600-45495800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr10:45489800-45492600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr10:45489800-45493400	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr10:45490000-45491600	Enhancers	Adipose Nuclei	Adipose
44	chr10:45490000-45491600	Enhancers	Liver	Liver
45	chr10:45490000-45491600	Enhancers	Stomach Smooth Muscle	stomach
46	chr10:45490000-45492200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr10:45490000-45492600	Enhancers	Primary T cells from cord blood	blood
48	chr10:45490000-45493200	Enhancers	Colon Smooth Muscle	Colon
49	chr10:45490000-45493600	Enhancers	Pancreas	Pancrea
50	chr10:45490000-45494000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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