Variant report

Variant	rs3740093
Chromosome Location	chr10:45499009-45499010
allele	C/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	MAFK	chr10:45498919-45499261	HepG2	liver:	n/a	chr10:45499066-45499081
2	MAFK	chr10:45498907-45499261	HepG2	liver:	n/a	chr10:45499066-45499081
3	MAFK	chr10:45498992-45499199	K562	blood:	n/a	chr10:45499066-45499081
4	MAFF	chr10:45498935-45499252	HepG2	liver:	n/a	chr10:45499064-45499082
5	KAP1	chr10:45498970-45499420	HEK293	kidney:	n/a	n/a
6	ZNF274	chr10:45498822-45499798	K562	blood:	n/a	n/a
7	MAFF	chr10:45498915-45499217	K562	blood:	n/a	chr10:45499064-45499082
8	ZNF274	chr10:45498787-45499555	GM08714	blood:	n/a	n/a
9	ZNF274	chr10:45498972-45499439	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr10:45496249-45499472	K562	blood:	n/a	n/a
11	KAP1	chr10:45498953-45499305	K562	blood:	n/a	n/a
12	SETDB1	chr10:45498947-45499387	U2OS	brain:	n/a	n/a
13	ZNF274	chr10:45498970-45499533	NT2-D1	testis:	n/a	n/a
14	MAFK	chr10:45498915-45499237	IMR90	lung:	n/a	chr10:45499066-45499081

No.	Distal block	Cell Line	Cell type
1	chr10:45495007..45496595-chr10:45497671..45499696,2	MCF-7	breast:
2	chr10:45495742..45497934-chr10:45498787..45500751,2	MCF-7	breast:
3	chr10:45466696..45473467-chr10:45492241..45499604,15	K562	blood:

Variant related genes	Relation type
C10orf25	TF binding region
ENSG00000107551	Chromatin interaction
ENSG00000165511	Chromatin interaction
ENSG00000165512	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11239303	0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11239305	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11239307	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11239308	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11239309	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11239311	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239315	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239319	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239323	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239324	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11239342	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239343	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11239345	1.00[EUR][1000 genomes]
rs11239346	1.00[EUR][1000 genomes]
rs12354652	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12358699	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12359377	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12359697	0.91[EUR][1000 genomes]
rs12412427	1.00[AFR][1000 genomes]
rs17157322	0.91[EUR][1000 genomes]
rs2274888	1.00[MEX][hapmap]
rs3740092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41301601	0.91[EUR][1000 genomes]
rs41301609	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41301611	0.97[EUR][1000 genomes]
rs41306544	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs41306546	0.91[EUR][1000 genomes]
rs59381196	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45497000-45511000	Weak transcription	Gastric	stomach
2	chr10:45497200-45499200	Weak transcription	Small Intestine	intestine
3	chr10:45497200-45500200	Weak transcription	Lung	lung
4	chr10:45497200-45504000	Weak transcription	Esophagus	oesophagus
5	chr10:45497400-45501200	Weak transcription	Aorta	Aorta
6	chr10:45497400-45501400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:45497400-45503800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr10:45497400-45504000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr10:45497400-45504000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr10:45497600-45499200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr10:45497600-45499200	Weak transcription	HSMMtube	muscle
12	chr10:45497600-45499600	ZNF genes & repeats	K562	blood
13	chr10:45497600-45499800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr10:45497600-45500200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr10:45497600-45502800	Weak transcription	Fetal Brain Male	brain
16	chr10:45497600-45503800	Weak transcription	Brain Substantia Nigra	brain
17	chr10:45497600-45504000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr10:45497800-45499200	Weak transcription	HepG2	liver
19	chr10:45497800-45499600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr10:45497800-45500600	ZNF genes & repeats	Primary B cells from cord blood	blood
21	chr10:45497800-45500600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
22	chr10:45497800-45502200	Weak transcription	Right Ventricle	heart
23	chr10:45497800-45504000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr10:45498000-45499200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr10:45498000-45499200	Weak transcription	Brain Anterior Caudate	brain
26	chr10:45498000-45499400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr10:45498000-45500000	ZNF genes & repeats	Primary T cells from cord blood	blood
28	chr10:45498000-45500000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
29	chr10:45498000-45500200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr10:45498200-45500600	ZNF genes & repeats	GM12878-XiMat	blood
31	chr10:45498200-45503800	Weak transcription	Colon Smooth Muscle	Colon
32	chr10:45498200-45503800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr10:45498200-45504000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr10:45498400-45499200	Weak transcription	Fetal Brain Female	brain
35	chr10:45498400-45499400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr10:45498400-45499400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr10:45498400-45499600	Genic enhancers	HUVEC	blood vessel
38	chr10:45498400-45500200	Weak transcription	Osteobl	bone
39	chr10:45498400-45500400	Genic enhancers	Primary hematopoietic stem cells	blood
40	chr10:45498400-45500600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
41	chr10:45498400-45501200	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr10:45498400-45503800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr10:45498600-45499200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
44	chr10:45498600-45499400	ZNF genes & repeats	HSMM	muscle
45	chr10:45498600-45499600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
46	chr10:45498600-45499600	Genic enhancers	Fetal Thymus	thymus
47	chr10:45498600-45499800	Genic enhancers	Dnd41	blood
48	chr10:45498600-45500400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr10:45498600-45500400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr10:45498600-45500800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood

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