Variant report

Variant	rs6507677
Chromosome Location	chr18:43762557-43762558
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:43753433..43756017-chr18:43759493..43763624,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152242	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11082514	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11082518	0.89[EUR][1000 genomes]
rs11082519	0.82[ASN][1000 genomes]
rs12457740	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12605945	0.90[EUR][1000 genomes]
rs12607898	0.90[EUR][1000 genomes]
rs12608232	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12709736	0.90[EUR][1000 genomes]
rs12962307	0.90[EUR][1000 genomes]
rs12962951	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12963787	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12963943	0.84[EUR][1000 genomes]
rs12969147	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13381496	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13381515	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13381523	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13381525	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13381529	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1808946	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36191490	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3744858	0.89[EUR][1000 genomes]
rs4335852	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4453594	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4453596	0.93[EUR][1000 genomes]
rs4542747	0.90[EUR][1000 genomes]
rs4574015	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4627465	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4890317	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4890319	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4890320	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4890321	0.89[EUR][1000 genomes]
rs4890626	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4890628	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4890629	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4890631	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4890632	0.90[EUR][1000 genomes]
rs4890633	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4890634	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4890635	0.81[ASN][1000 genomes]
rs55747741	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62096523	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62096524	0.90[EUR][1000 genomes]
rs62096525	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62096526	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62098160	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6507670	0.87[EUR][1000 genomes]
rs6507676	0.90[EUR][1000 genomes]
rs6507680	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6507681	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6507682	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6507690	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6507691	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6507692	0.90[EUR][1000 genomes]
rs6507693	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs718513	0.88[EUR][1000 genomes]
rs718514	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7227847	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7228365	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7230154	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7230995	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7231430	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7231820	0.90[EUR][1000 genomes]
rs7234695	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7236687	0.89[EUR][1000 genomes]
rs7239351	0.89[EUR][1000 genomes]
rs7240354	0.81[EUR][1000 genomes]
rs7241527	0.89[EUR][1000 genomes]
rs7241829	0.90[EUR][1000 genomes]
rs7242375	0.86[EUR][1000 genomes]
rs7245091	0.92[EUR][1000 genomes]
rs73425119	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8084309	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8084827	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8084829	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8085138	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8086610	0.88[EUR][1000 genomes]
rs8086956	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8090542	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8093407	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8094070	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8094706	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8095142	0.87[EUR][1000 genomes]
rs8095729	0.92[EUR][1000 genomes]
rs8095799	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8098751	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8099202	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9675387	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9807157	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9944715	0.90[EUR][1000 genomes]
rs9944767	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9944836	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9945783	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9947206	0.89[EUR][1000 genomes]
rs9948282	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9949494	0.90[EUR][1000 genomes]
rs9951624	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9952469	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9952654	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9956574	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9959813	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9959905	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9960378	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9963153	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][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	nsv978710	chr18:43759964-43770866	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6507677	C18orf25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43755000-43766800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr18:43755000-43769600	Weak transcription	Gastric	stomach
3	chr18:43755200-43780400	Weak transcription	Aorta	Aorta
4	chr18:43755600-43762600	Enhancers	Primary T cells fromperipheralblood	blood
5	chr18:43755600-43762600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr18:43755600-43763000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr18:43755600-43764600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr18:43755600-43766800	Weak transcription	Fetal Intestine Small	intestine
9	chr18:43755600-43768000	Weak transcription	Fetal Intestine Large	intestine
10	chr18:43755600-43776200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr18:43755600-43795600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr18:43755800-43762600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr18:43755800-43765800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr18:43755800-43766000	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr18:43755800-43776800	Weak transcription	Fetal Muscle Leg	muscle
16	chr18:43755800-43779600	Weak transcription	Thymus	Thymus
17	chr18:43756000-43763000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr18:43756000-43771000	Weak transcription	NHDF-Ad	bronchial
19	chr18:43756200-43762800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr18:43756200-43763800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr18:43756200-43765800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr18:43756400-43764400	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr18:43756400-43765600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr18:43756400-43766600	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr18:43756600-43762600	Weak transcription	Primary B cells from cord blood	blood
26	chr18:43756600-43764400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr18:43756600-43765600	Weak transcription	HepG2	liver
28	chr18:43756600-43771600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr18:43756800-43796000	Weak transcription	Esophagus	oesophagus
30	chr18:43757600-43765600	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr18:43758000-43782200	Weak transcription	Right Ventricle	heart
32	chr18:43758200-43762800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr18:43758200-43764000	Weak transcription	Spleen	Spleen
34	chr18:43758400-43767000	Weak transcription	Fetal Stomach	stomach
35	chr18:43758800-43773000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr18:43758800-43775000	Weak transcription	Dnd41	blood
37	chr18:43758800-43785000	Weak transcription	Fetal Thymus	thymus
38	chr18:43759200-43764000	Weak transcription	Lung	lung
39	chr18:43759200-43766800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr18:43759800-43763800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr18:43760200-43763400	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr18:43760400-43762800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr18:43760600-43763200	Enhancers	Primary hematopoietic stem cells	blood
44	chr18:43761000-43762600	Enhancers	Psoas Muscle	Psoas
45	chr18:43761000-43762800	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr18:43761000-43763800	Enhancers	Liver	Liver
47	chr18:43761200-43762600	Enhancers	Hela-S3	cervix
48	chr18:43761200-43762800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr18:43761200-43763200	Enhancers	Primary T cells from cord blood	blood
50	chr18:43761200-43765600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links