Variant report

Variant	rs9955853
Chromosome Location	chr18:43829655-43829656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:43752714..43757131-chr18:43829030..43833510,5	MCF-7	breast:
2	chr18:43829216..43831646-chr18:43834393..43837026,3	K562	blood:
3	chr18:43822903..43824970-chr18:43829081..43831367,2	K562	blood:
4	chr18:43823470..43825591-chr18:43828533..43831367,2	K562	blood:

Variant related genes	Relation type
ENSG00000152242	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11664314	1.00[JPT][hapmap]
rs11664743	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11874712	1.00[JPT][hapmap]
rs12454696	0.81[ASN][1000 genomes]
rs12955201	1.00[JPT][hapmap]
rs12959752	1.00[JPT][hapmap]
rs17758799	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55880723	0.83[ASN][1000 genomes]
rs718515	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7240076	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7359798	1.00[JPT][hapmap]
rs7359800	1.00[JPT][hapmap]
rs8089153	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs8095374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9807399	1.00[JPT][hapmap]
rs9947316	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9964524	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064031	chr18:43782309-43878806	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9955853	C18orf25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43797000-43833400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr18:43798800-43833800	Weak transcription	HepG2	liver
3	chr18:43799000-43834000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr18:43802800-43830000	Weak transcription	Brain Substantia Nigra	brain
5	chr18:43805400-43829800	Weak transcription	Fetal Intestine Large	intestine
6	chr18:43810200-43832400	Weak transcription	Aorta	Aorta
7	chr18:43815200-43830000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr18:43815400-43830000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr18:43815400-43830000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr18:43815400-43830200	Weak transcription	Gastric	stomach
11	chr18:43815800-43830000	Weak transcription	Brain Angular Gyrus	brain
12	chr18:43817600-43829800	Weak transcription	Pancreas	Pancrea
13	chr18:43817600-43830200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr18:43820400-43829800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr18:43820400-43830000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr18:43820400-43830000	Weak transcription	Brain Anterior Caudate	brain
17	chr18:43820600-43829800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr18:43820600-43830000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr18:43820600-43833400	Weak transcription	Ovary	ovary
20	chr18:43823600-43830000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr18:43823600-43830600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr18:43824200-43830600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr18:43824600-43829800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr18:43825200-43829800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr18:43825200-43830800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr18:43825400-43844200	Weak transcription	Fetal Brain Female	brain
27	chr18:43825800-43834000	Weak transcription	Liver	Liver
28	chr18:43826000-43830200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr18:43826200-43840000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr18:43826400-43830000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr18:43826400-43830000	Weak transcription	Colon Smooth Muscle	Colon
32	chr18:43826400-43830200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr18:43826600-43847000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr18:43826800-43843600	Weak transcription	Brain Germinal Matrix	brain
35	chr18:43827600-43829800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr18:43827600-43830000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr18:43827800-43829800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr18:43827800-43830000	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr18:43828000-43830200	Weak transcription	Fetal Lung	lung
40	chr18:43828200-43830000	Enhancers	Primary B cells from peripheral blood	blood
41	chr18:43828200-43830000	Enhancers	Primary T cells fromperipheralblood	blood
42	chr18:43828200-43830000	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr18:43828200-43839600	Weak transcription	Right Atrium	heart
44	chr18:43828400-43829800	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr18:43828400-43829800	Weak transcription	Fetal Thymus	thymus
46	chr18:43828400-43829800	Enhancers	Placenta Amnion	Placenta Amnion
47	chr18:43828400-43839600	Weak transcription	Fetal Stomach	stomach
48	chr18:43828600-43829800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr18:43828600-43830000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr18:43828600-43830000	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links