Variant report

Variant	rs6507676
Chromosome Location	chr18:43739730-43739731
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:43738327..43740955-chr18:43753393..43757387,3	K562	blood:
2	chr18:43739084..43741230-chr18:43849906..43852814,2	MCF-7	breast:
3	chr18:43734389..43736469-chr18:43738925..43741638,2	K562	blood:
4	chr18:43737408..43740388-chr18:43753340..43756305,2	MCF-7	breast:
5	chr18:43737274..43740808-chr18:43743421..43745536,3	K562	blood:
6	chr18:43737434..43740095-chr18:43752328..43754121,3	MCF-7	breast:
7	chr18:43737450..43741302-chr18:43741650..43744283,3	MCF-7	breast:
8	chr18:43731595..43733351-chr18:43739410..43741644,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000152242	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs11082512	0.87[EUR][1000 genomes]
rs11082514	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11082518	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12457740	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12605945	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12607898	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12608232	0.84[EUR][1000 genomes]
rs12709736	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12962307	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12962951	0.84[EUR][1000 genomes]
rs12963787	0.82[EUR][1000 genomes]
rs12963943	0.87[ASN][1000 genomes]
rs12967694	0.87[EUR][1000 genomes]
rs12969147	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13381496	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13381515	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13381523	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13381525	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13381529	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1808946	0.84[EUR][1000 genomes]
rs36191490	0.85[EUR][1000 genomes]
rs3744858	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4335852	0.89[EUR][1000 genomes]
rs4453594	0.84[EUR][1000 genomes]
rs4453596	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4542747	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4574015	0.84[EUR][1000 genomes]
rs4627465	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4890317	0.89[EUR][1000 genomes]
rs4890319	0.84[EUR][1000 genomes]
rs4890320	0.84[EUR][1000 genomes]
rs4890321	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4890628	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4890629	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4890631	0.84[EUR][1000 genomes]
rs4890632	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4890633	0.85[EUR][1000 genomes]
rs4890634	0.81[EUR][1000 genomes]
rs55747741	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62096523	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62096524	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62096525	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62096526	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6507670	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6507675	0.84[ASN][1000 genomes]
rs6507677	0.90[EUR][1000 genomes]
rs6507680	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6507681	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6507682	0.89[EUR][1000 genomes]
rs6507690	0.85[EUR][1000 genomes]
rs6507691	0.83[EUR][1000 genomes]
rs6507692	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6507693	0.84[EUR][1000 genomes]
rs718513	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs718514	0.82[EUR][1000 genomes]
rs7227847	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7228365	0.85[EUR][1000 genomes]
rs7230154	0.85[EUR][1000 genomes]
rs7230995	0.84[EUR][1000 genomes]
rs7231430	0.85[EUR][1000 genomes]
rs7231820	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7234695	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7236687	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7239351	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7240354	0.88[ASN][1000 genomes]
rs7241527	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7241829	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7241983	0.80[ASN][1000 genomes]
rs7242375	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7245091	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73425119	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8084309	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8084827	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8084829	0.82[EUR][1000 genomes]
rs8085138	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8086610	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8086956	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8090542	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8093407	0.84[EUR][1000 genomes]
rs8094070	0.84[EUR][1000 genomes]
rs8094706	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8095142	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8095729	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8095799	0.85[EUR][1000 genomes]
rs8098751	0.82[EUR][1000 genomes]
rs8099202	0.85[EUR][1000 genomes]
rs9675387	0.84[EUR][1000 genomes]
rs9807157	0.85[EUR][1000 genomes]
rs9944715	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9944767	0.81[EUR][1000 genomes]
rs9944836	0.85[EUR][1000 genomes]
rs9945783	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9947206	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9948282	0.87[EUR][1000 genomes]
rs9949494	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9951624	0.84[EUR][1000 genomes]
rs9952469	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9952654	0.83[EUR][1000 genomes]
rs9956574	0.85[EUR][1000 genomes]
rs9959813	0.84[EUR][1000 genomes]
rs9959905	0.85[EUR][1000 genomes]
rs9960378	0.85[EUR][1000 genomes]
rs9963153	0.84[EUR][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	nsv1062024	chr18:43589516-43749410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv543694	chr18:43589516-43749410	Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6507676	C18orf25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43706200-43747800	Weak transcription	Brain Substantia Nigra	brain
2	chr18:43710600-43752800	Weak transcription	Fetal Brain Female	brain
3	chr18:43714000-43748400	Weak transcription	Ovary	ovary
4	chr18:43733200-43740200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr18:43733200-43740600	Enhancers	HMEC	breast
6	chr18:43733200-43753200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr18:43733600-43746200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr18:43733600-43746400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr18:43733800-43744200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr18:43733800-43746200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr18:43734200-43746200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr18:43734600-43740600	Enhancers	NHEK	skin
13	chr18:43736400-43740400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr18:43736400-43742400	Enhancers	Primary T cells fromperipheralblood	blood
15	chr18:43736400-43742400	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr18:43736400-43747800	Weak transcription	Thymus	Thymus
17	chr18:43736800-43740200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr18:43736800-43740400	Weak transcription	NH-A	brain
19	chr18:43736800-43746200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr18:43737200-43747800	Weak transcription	Spleen	Spleen
21	chr18:43737200-43749200	Weak transcription	HSMMtube	muscle
22	chr18:43737200-43749400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr18:43737600-43739800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr18:43737600-43740000	Weak transcription	HepG2	liver
25	chr18:43737600-43740200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr18:43737600-43740600	Weak transcription	Fetal Thymus	thymus
27	chr18:43737600-43742000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr18:43737600-43753000	Weak transcription	Fetal Stomach	stomach
29	chr18:43737800-43740400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr18:43738000-43740000	Weak transcription	Primary T cells from cord blood	blood
31	chr18:43738600-43739800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr18:43738800-43740000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr18:43738800-43740400	Weak transcription	Dnd41	blood
34	chr18:43738800-43740400	Weak transcription	Osteobl	bone
35	chr18:43739000-43739800	Weak transcription	Placenta	Placenta
36	chr18:43739000-43739800	Enhancers	Hela-S3	cervix
37	chr18:43739000-43740000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr18:43739000-43740000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr18:43739000-43740000	Weak transcription	A549	lung
40	chr18:43739000-43740200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr18:43739000-43742000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr18:43739000-43742000	Weak transcription	K562	blood
43	chr18:43739000-43743800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr18:43739000-43753200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr18:43739200-43741800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr18:43739400-43739800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr18:43739600-43741200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr18:43739600-43741200	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr18:43739600-43742200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr18:43739600-43742400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links