Variant report

Variant	rs10838518
Chromosome Location	chr11:45834466-45834467
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	POLR2A	chr11:45834102-45834924	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr11:45834410-45834692	HCT-116	colon:	n/a	n/a
3	POLR2A	chr11:45833967-45835192	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr11:45834341-45834897	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr11:45833433-45835840	MCF-7	breast:	n/a	n/a
6	POLR2A	chr11:45834387-45835152	HepG2	liver:	n/a	n/a
7	POLR2A	chr11:45834121-45834936	GM12878	blood:	n/a	n/a
8	POLR2A	chr11:45832990-45836303	K562	blood:	n/a	n/a
9	POLR2A	chr11:45833918-45835059	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr11:45834139-45834675	HepG2	liver:	n/a	n/a
11	POLR2A	chr11:45834242-45836230	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr11:45833221-45835005	A549	lung:	n/a	n/a
13	POLR2A	chr11:45834243-45835109	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr11:45834120-45835080	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:45833116..45834874-chr11:45867735..45869641,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255447	TF binding region
ENSG00000121671	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10838523	0.85[AMR][1000 genomes]
rs12281674	0.87[AMR][1000 genomes]
rs12284956	0.87[AMR][1000 genomes]
rs16938376	0.91[ASN][1000 genomes]
rs2037311	0.87[AMR][1000 genomes]
rs60935266	0.94[ASN][1000 genomes]
rs7127456	1.00[ASN][1000 genomes]
rs73466394	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73468311	0.82[AMR][1000 genomes]
rs9300053	0.82[AMR][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	nsv897314	chr11:45816020-45965129	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv897315	chr11:45817637-45838926	Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 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	chr11:45828000-45837200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr11:45828000-45837200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:45829200-45835000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:45829600-45834800	Strong transcription	Primary T cells from cord blood	blood
5	chr11:45829600-45834800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr11:45829600-45834800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:45829600-45835000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr11:45829600-45835200	Strong transcription	Fetal Stomach	stomach
9	chr11:45829600-45835800	Weak transcription	HSMM	muscle
10	chr11:45829600-45836000	Weak transcription	HepG2	liver
11	chr11:45829800-45834600	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr11:45829800-45835400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr11:45830000-45834600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:45830000-45834600	Weak transcription	Small Intestine	intestine
15	chr11:45830200-45834800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:45830200-45835000	Strong transcription	Fetal Intestine Small	intestine
17	chr11:45831200-45835000	Strong transcription	Fetal Muscle Leg	muscle
18	chr11:45831200-45837600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:45831400-45834800	Weak transcription	K562	blood
20	chr11:45831600-45834600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr11:45831600-45835000	Strong transcription	Dnd41	blood
22	chr11:45831600-45837400	Weak transcription	Hela-S3	cervix
23	chr11:45831800-45834600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr11:45831800-45834600	Strong transcription	Fetal Muscle Trunk	muscle
25	chr11:45831800-45834600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr11:45831800-45835000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr11:45832000-45834800	Strong transcription	Fetal Brain Female	brain
28	chr11:45832000-45838600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr11:45832200-45839600	Weak transcription	Fetal Heart	heart
30	chr11:45832400-45834600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr11:45832400-45834600	Strong transcription	Lung	lung
32	chr11:45832800-45834600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr11:45832800-45834600	Strong transcription	NH-A	brain
34	chr11:45832800-45837200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr11:45833000-45834800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr11:45833000-45837200	Weak transcription	A549	lung
37	chr11:45833200-45834600	Genic enhancers	Placenta	Placenta
38	chr11:45833200-45834800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr11:45833200-45835400	Weak transcription	Psoas Muscle	Psoas
40	chr11:45833400-45835000	Weak transcription	Brain Substantia Nigra	brain
41	chr11:45833400-45835200	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr11:45833400-45835400	Weak transcription	Colon Smooth Muscle	Colon
43	chr11:45833600-45835000	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr11:45833600-45835400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr11:45833600-45835800	Weak transcription	HUVEC	blood vessel
46	chr11:45833600-45837200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr11:45833600-45848000	Weak transcription	Right Ventricle	heart
48	chr11:45833800-45834800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr11:45833800-45835600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr11:45833800-45835600	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links