Variant report

Variant	rs41274300
Chromosome Location	chr18:9119489-9119490
allele	A/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	chr18:9119414-9119705	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:9102444..9104093-chr18:9117938..9120762,2	MCF-7	breast:
2	chr18:9117343..9120126-chr18:9132921..9134783,2	K562	blood:

Variant related genes	Relation type
ENSG00000263847	TF binding region
ENSG00000178127	Chromatin interaction
ENSG00000266053	Chromatin interaction
ENSG00000265257	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10502390	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10853373	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11081459	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11081463	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11660889	0.90[AMR][1000 genomes]
rs11661921	0.80[AMR][1000 genomes]
rs11663175	0.90[AMR][1000 genomes]
rs11663949	0.87[AMR][1000 genomes]
rs11872176	0.84[AMR][1000 genomes]
rs11872481	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11875086	0.90[AMR][1000 genomes]
rs11876775	0.90[AMR][1000 genomes]
rs11876821	0.90[AMR][1000 genomes]
rs11877843	0.90[AMR][1000 genomes]
rs12454025	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12454908	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12454936	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12455304	0.81[AMR][1000 genomes]
rs12457266	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12457429	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12966444	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12966775	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12968060	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35002591	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35587943	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35774167	0.93[AMR][1000 genomes]
rs35849084	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62085924	0.84[AMR][1000 genomes]
rs62085926	0.84[AMR][1000 genomes]
rs6506641	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71362073	0.84[AMR][1000 genomes]
rs7226632	0.90[AMR][1000 genomes]
rs7229685	0.81[AMR][1000 genomes]
rs8085549	0.82[AMR][1000 genomes]
rs8085669	0.87[AMR][1000 genomes]
rs8089577	0.84[AMR][1000 genomes]
rs8090297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8095601	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];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	nsv1064883	chr18:8709670-9133224	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv431971	chr18:9081185-9326852	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1056258	chr18:9094498-9181498	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv909364	chr18:9114096-9186684	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9104400-9130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:9106200-9123200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr18:9107000-9135200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr18:9107400-9135400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr18:9107600-9123200	Weak transcription	Thymus	Thymus
6	chr18:9107800-9134600	Weak transcription	Fetal Brain Male	brain
7	chr18:9108200-9123000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr18:9108200-9127200	Weak transcription	Fetal Brain Female	brain
9	chr18:9109600-9123200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr18:9111200-9125400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr18:9111600-9126800	Weak transcription	Colonic Mucosa	Colon
12	chr18:9111800-9123400	Weak transcription	Fetal Stomach	stomach
13	chr18:9113000-9119800	Enhancers	Brain Hippocampus Middle	brain
14	chr18:9114000-9119600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr18:9114000-9121000	Weak transcription	Fetal Muscle Leg	muscle
16	chr18:9114000-9123200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr18:9114000-9123400	Weak transcription	Fetal Intestine Small	intestine
18	chr18:9114000-9127400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr18:9114000-9130800	Weak transcription	Ovary	ovary
20	chr18:9115400-9134600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr18:9115600-9119600	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr18:9115600-9119800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr18:9115800-9134800	Strong transcription	Dnd41	blood
24	chr18:9116000-9119600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr18:9116600-9119800	Enhancers	Brain Cingulate Gyrus	brain
26	chr18:9116600-9120400	Enhancers	Brain Substantia Nigra	brain
27	chr18:9116800-9119800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr18:9116800-9135200	Strong transcription	Fetal Thymus	thymus
29	chr18:9117200-9119600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr18:9117200-9134800	Weak transcription	Brain Germinal Matrix	brain
31	chr18:9117400-9123400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr18:9117400-9125800	Weak transcription	Right Atrium	heart
33	chr18:9117400-9132000	Strong transcription	Fetal Intestine Large	intestine
34	chr18:9117400-9135200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr18:9117400-9135600	Weak transcription	Esophagus	oesophagus
36	chr18:9117400-9135800	Weak transcription	Gastric	stomach
37	chr18:9117600-9119800	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr18:9117600-9123400	Weak transcription	Left Ventricle	heart
39	chr18:9117600-9123400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr18:9117600-9127400	Weak transcription	Spleen	Spleen
41	chr18:9117600-9134800	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr18:9117600-9135200	Weak transcription	Psoas Muscle	Psoas
43	chr18:9117600-9135800	Weak transcription	Pancreas	Pancrea
44	chr18:9117800-9119600	Weak transcription	A549	lung
45	chr18:9117800-9120200	Enhancers	HSMMtube	muscle
46	chr18:9117800-9122400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr18:9117800-9124000	Strong transcription	HepG2	liver
48	chr18:9117800-9127200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr18:9117800-9128800	Weak transcription	Lung	lung
50	chr18:9117800-9132600	Weak transcription	Aorta	Aorta

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