Variant report

Variant	rs74090646
Chromosome Location	chr1:78019442-78019443
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	RCOR1	chr1:78019220-78019665	K562	blood:	n/a	n/a
2	UBTF	chr1:78019440-78019533	K562	blood:	n/a	n/a
3	BHLHE40	chr1:78019351-78019629	K562	blood:	n/a	n/a
4	KAP1	chr1:78019105-78019668	U2OS	brain:	n/a	n/a
5	ZNF263	chr1:78019156-78019706	HEK293-T-REx	kidney:	n/a	chr1:78019511-78019520 chr1:78019497-78019518
6	POLR2A	chr1:78019258-78019518	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78017249..78019893-chr17:59489545..59491319,2	MCF-7	breast:

Variant related genes	Relation type
AK5	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs35178440	1.00[EUR][1000 genomes]
rs55790102	1.00[AFR][1000 genomes]
rs55872024	1.00[EUR][1000 genomes]
rs58120905	1.00[EUR][1000 genomes]
rs59338720	1.00[EUR][1000 genomes]
rs59883033	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60000721	1.00[EUR][1000 genomes]
rs60939723	1.00[EUR][1000 genomes]
rs61553400	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61655329	1.00[EUR][1000 genomes]
rs74090643	0.86[AFR][1000 genomes]
rs74090649	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74090651	0.86[AFR][1000 genomes]
rs74090653	1.00[EUR][1000 genomes]
rs74090654	1.00[AFR][1000 genomes]
rs74090658	0.86[AFR][1000 genomes]
rs74090661	1.00[AFR][1000 genomes]
rs74090669	1.00[EUR][1000 genomes]
rs74090673	1.00[EUR][1000 genomes]
rs74090678	1.00[EUR][1000 genomes]
rs74090686	1.00[EUR][1000 genomes]
rs74092304	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv871143	chr1:77955577-78031994	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1533	chr1:77990504-78036279	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv870709	chr1:78016517-78198322	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78000000-78030600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:78000000-78031200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr1:78005600-78034800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:78005800-78026200	Weak transcription	Left Ventricle	heart
5	chr1:78005800-78032400	Weak transcription	Psoas Muscle	Psoas
6	chr1:78006000-78022400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:78006000-78026200	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:78006000-78031000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:78006200-78024400	Weak transcription	HSMMtube	muscle
10	chr1:78006200-78027200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:78006200-78064400	Weak transcription	Stomach Mucosa	stomach
12	chr1:78007800-78028400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:78009000-78023200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:78010000-78027400	Weak transcription	A549	lung
15	chr1:78011800-78021000	Weak transcription	HSMM	muscle
16	chr1:78012000-78019800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:78012000-78031000	Weak transcription	Brain Angular Gyrus	brain
18	chr1:78012200-78021000	Weak transcription	NHLF	lung
19	chr1:78012200-78023000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:78012200-78023800	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr1:78012600-78022600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:78012600-78023000	Weak transcription	Osteobl	bone
23	chr1:78012600-78031000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:78012800-78023000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:78014200-78024200	Weak transcription	Brain Substantia Nigra	brain
26	chr1:78014200-78026000	Weak transcription	Brain Anterior Caudate	brain
27	chr1:78014400-78022600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:78014400-78024200	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:78014400-78030600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:78014400-78031800	Weak transcription	Right Ventricle	heart
31	chr1:78014600-78022600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:78014600-78023200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:78014600-78024600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:78014600-78027800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr1:78015800-78024400	Weak transcription	Fetal Intestine Small	intestine
36	chr1:78016000-78030600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:78016400-78021000	Weak transcription	NHDF-Ad	bronchial
38	chr1:78017200-78020200	Strong transcription	Primary T cells from cord blood	blood
39	chr1:78017400-78020200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:78017400-78023400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr1:78017800-78031000	Weak transcription	HepG2	liver
42	chr1:78018600-78021600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:78019200-78019600	Enhancers	Fetal Heart	heart
44	chr1:78019200-78019800	Strong transcription	Brain Cingulate Gyrus	brain
45	chr1:78019200-78019800	Enhancers	K562	blood
46	chr1:78019200-78026200	Weak transcription	NH-A	brain
47	chr1:78019200-78027200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:78019400-78020200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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