Variant report

Variant	rs74090649
Chromosome Location	chr1:78023082-78023083
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78020809..78023858-chr1:78146827..78149846,3	K562	blood:

Variant related genes	Relation type
ENSG00000036549	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs35178440	1.00[EUR][1000 genomes]
rs55790102	1.00[AFR][1000 genomes]
rs55872024	1.00[EUR][1000 genomes]
rs56010524	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]
rs60658102	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]
rs74090646	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]
rs74092305	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:87 , 50 per page) page: 1 2

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	chr1:78006000-78026200	Weak transcription	Fetal Muscle Leg	muscle
7	chr1:78006000-78031000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:78006200-78024400	Weak transcription	HSMMtube	muscle
9	chr1:78006200-78027200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:78006200-78064400	Weak transcription	Stomach Mucosa	stomach
11	chr1:78007800-78028400	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr1:78009000-78023200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:78010000-78027400	Weak transcription	A549	lung
14	chr1:78012000-78031000	Weak transcription	Brain Angular Gyrus	brain
15	chr1:78012200-78023800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:78012600-78031000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:78014200-78024200	Weak transcription	Brain Substantia Nigra	brain
18	chr1:78014200-78026000	Weak transcription	Brain Anterior Caudate	brain
19	chr1:78014400-78024200	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:78014400-78030600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:78014400-78031800	Weak transcription	Right Ventricle	heart
22	chr1:78014600-78023200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:78014600-78024600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:78014600-78027800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:78015800-78024400	Weak transcription	Fetal Intestine Small	intestine
26	chr1:78016000-78030600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:78017400-78023400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:78017800-78031000	Weak transcription	HepG2	liver
29	chr1:78019200-78026200	Weak transcription	NH-A	brain
30	chr1:78019200-78027200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:78019600-78031200	Weak transcription	Fetal Heart	heart
32	chr1:78019800-78026000	Weak transcription	NHEK	skin
33	chr1:78019800-78028400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:78019800-78029200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:78019800-78031200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:78019800-78031200	Weak transcription	K562	blood
37	chr1:78020000-78028400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:78020200-78024600	Weak transcription	Gastric	stomach
39	chr1:78020200-78025800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:78021400-78023400	Enhancers	HUVEC	blood vessel
41	chr1:78021600-78024600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:78021600-78026400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:78021600-78030600	Weak transcription	Adipose Nuclei	Adipose
44	chr1:78021800-78024600	Weak transcription	NHLF	lung
45	chr1:78021800-78026400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr1:78021800-78028400	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr1:78022000-78023600	Weak transcription	HSMM	muscle
48	chr1:78022000-78024400	Weak transcription	GM12878-XiMat	blood
49	chr1:78022200-78024000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:78022200-78026000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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