Variant report

Variant	rs61778380
Chromosome Location	chr1:10409956-10409957
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	chr1:10400783..10405636-chr1:10406745..10410852,7	K562	blood:

Variant related genes	Relation type
ENSG00000054523	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs59661672	1.00[AMR][1000 genomes]
rs60490329	1.00[AMR][1000 genomes]
rs61775871	1.00[AMR][1000 genomes]
rs61775875	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61775876	1.00[AMR][1000 genomes]
rs61775877	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61775888	1.00[AMR][1000 genomes]
rs61775891	1.00[AMR][1000 genomes]
rs61775893	1.00[AMR][1000 genomes]
rs61775919	1.00[AMR][1000 genomes]
rs61775921	1.00[AMR][1000 genomes]
rs61775979	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61778374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61778405	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61778417	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6541088	1.00[AMR][1000 genomes]
rs6541093	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6661175	1.00[AMR][1000 genomes]
rs6669000	1.00[AMR][1000 genomes]
rs6681412	1.00[AMR][1000 genomes]
rs7551816	1.00[AMR][1000 genomes]
rs7553321	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv545381	chr1:10296452-10423988	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10364600-10431000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:10380400-10436600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:10380600-10426400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:10381000-10436400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:10385200-10436400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:10386000-10434800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:10386400-10421600	Weak transcription	Hela-S3	cervix
8	chr1:10393200-10415800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:10393200-10431200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:10393600-10430800	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:10393800-10444600	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:10394200-10410000	Strong transcription	Fetal Brain Female	brain
13	chr1:10394200-10410000	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr1:10394200-10411400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:10394200-10413200	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr1:10394200-10414200	Strong transcription	Brain Germinal Matrix	brain
17	chr1:10394200-10414200	Strong transcription	Stomach Smooth Muscle	stomach
18	chr1:10394200-10415800	Strong transcription	Adipose Nuclei	Adipose
19	chr1:10394200-10415800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr1:10394200-10441800	Strong transcription	Liver	Liver
21	chr1:10394400-10410000	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr1:10394400-10411200	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:10394400-10411400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:10394400-10413400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:10394400-10414200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr1:10395600-10425200	Weak transcription	Thymus	Thymus
27	chr1:10397600-10421000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:10397800-10410600	Weak transcription	Right Ventricle	heart
29	chr1:10397800-10425400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr1:10397800-10434800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr1:10398000-10421000	Weak transcription	NHEK	skin
32	chr1:10398000-10438000	Weak transcription	GM12878-XiMat	blood
33	chr1:10398400-10425400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:10399000-10420800	Weak transcription	NHLF	lung
35	chr1:10400000-10410000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:10400000-10416200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:10400200-10413600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:10400200-10438200	Weak transcription	Stomach Mucosa	stomach
39	chr1:10400600-10434600	Weak transcription	K562	blood
40	chr1:10400600-10446400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:10400600-10447400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:10400800-10414000	Strong transcription	Fetal Muscle Leg	muscle
43	chr1:10401600-10412600	Strong transcription	Brain Angular Gyrus	brain
44	chr1:10401600-10420800	Weak transcription	Fetal Heart	heart
45	chr1:10401600-10421000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:10401800-10415200	Strong transcription	HSMMtube	muscle
47	chr1:10402200-10418400	Weak transcription	A549	lung
48	chr1:10402600-10410800	Weak transcription	HUVEC	blood vessel
49	chr1:10402600-10437200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr1:10403000-10413600	Strong transcription	Fetal Stomach	stomach

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