Variant report

Variant	rs55867821
Chromosome Location	chr1:46771622-46771623
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:46771571-46771672	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:46771595-46771779	K562	blood:	n/a	n/a
3	POLR2A	chr1:46771010-46771798	K562	blood:	n/a	n/a
4	POLR2A	chr1:46771610-46772107	K562	blood:	n/a	n/a
5	POLR2A	chr1:46771611-46772095	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46763061..46775715-chr1:46803221..46815018,50	K562	blood:
2	chr1:46763061..46775205-chr1:46803159..46817121,53	K562	blood:
3	chr1:46767029..46769765-chr1:46770513..46776253,5	MCF-7	breast:
4	chr1:46761317..46766795-chr1:46767207..46772068,9	MCF-7	breast:
5	chr1:46711557..46715191-chr1:46765613..46771974,14	K562	blood:

No data

Variant related genes	Relation type
UQCRH	TF binding region
LRRC41	TF binding region
ENSG00000117481	Chromatin interaction
ENSG00000085999	Chromatin interaction
ENSG00000173660	Chromatin interaction
ENSG00000132128	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11211256	1.00[AMR][1000 genomes]
rs12072566	1.00[AMR][1000 genomes]
rs41292143	1.00[AMR][1000 genomes]
rs45508501	1.00[AMR][1000 genomes]
rs72897003	1.00[AMR][1000 genomes]
rs72897033	1.00[AMR][1000 genomes]
rs74072314	1.00[AMR][1000 genomes]
rs9782966	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	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers 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	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv470711	chr1:46660295-46810530	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv947254	chr1:46769363-46808918	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46766400-46772400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:46766600-46773000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr1:46766800-46771800	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr1:46767200-46771800	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr1:46767200-46772000	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr1:46767400-46771800	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:46767600-46772400	Active TSS	Right Ventricle	heart
8	chr1:46770000-46771800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:46770200-46772600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:46770400-46773000	Enhancers	Liver	Liver
11	chr1:46770400-46775400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:46770600-46771800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr1:46770600-46771800	Enhancers	Brain Angular Gyrus	brain
14	chr1:46770600-46772600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:46770600-46772600	Weak transcription	Lung	lung
16	chr1:46770600-46773000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:46770600-46773000	Weak transcription	Brain Anterior Caudate	brain
18	chr1:46770600-46773000	Enhancers	Fetal Thymus	thymus
19	chr1:46770600-46773200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr1:46770600-46773200	Enhancers	Primary T cells fromperipheralblood	blood
21	chr1:46770600-46773200	Enhancers	Fetal Heart	heart
22	chr1:46770600-46773600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr1:46770600-46773800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:46770600-46774000	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr1:46770600-46774600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:46770600-46774800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:46770600-46775400	Weak transcription	Fetal Kidney	kidney
28	chr1:46770600-46775400	Weak transcription	Spleen	Spleen
29	chr1:46770600-46775600	Weak transcription	HSMMtube	muscle
30	chr1:46770600-46781000	Strong transcription	Fetal Intestine Small	intestine
31	chr1:46770600-46783600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr1:46770800-46771800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:46770800-46771800	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr1:46770800-46771800	Enhancers	Ovary	ovary
35	chr1:46770800-46772400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:46770800-46772400	Weak transcription	Colon Smooth Muscle	Colon
37	chr1:46770800-46772800	Weak transcription	Fetal Brain Female	brain
38	chr1:46770800-46773200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:46770800-46773200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:46770800-46773200	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr1:46770800-46773200	Weak transcription	Osteobl	bone
42	chr1:46770800-46773400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:46770800-46774800	Weak transcription	NHLF	lung
44	chr1:46770800-46775400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:46770800-46775400	Weak transcription	Small Intestine	intestine
46	chr1:46770800-46775600	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:46770800-46775600	Weak transcription	NHDF-Ad	bronchial
48	chr1:46770800-46787000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr1:46771000-46771800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:46771000-46771800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links