Variant report

Variant	rs2286090
Chromosome Location	chr7:38789862-38789863
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38787918..38790102-chr7:38792675..38794796,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10232480	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951570	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11978728	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12538785	0.99[ASN][1000 genomes]
rs12701660	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13244313	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1859937	0.81[EUR][1000 genomes]
rs1978170	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2074656	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2240350	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240355	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286081	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2286083	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286085	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286095	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286097	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286099	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286100	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286102	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2392595	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3207255	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3779126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801135	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3801142	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3801144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4720298	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4720299	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4723783	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4723793	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6462858	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6462859	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6462861	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6462862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6961672	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7785056	0.82[ASN][1000 genomes]
rs7788664	0.82[EUR][1000 genomes]
rs7794371	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7806860	0.84[AMR][1000 genomes]
rs7811599	0.82[AMR][1000 genomes];0.81[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	nsv887965	chr7:38706384-38793243	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 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	chr7:38749000-38803600	Weak transcription	Fetal Brain Male	brain
2	chr7:38755000-38791200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:38757200-38835400	Weak transcription	Psoas Muscle	Psoas
4	chr7:38759200-38810200	Weak transcription	A549	lung
5	chr7:38759400-38810600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr7:38760000-38799800	Weak transcription	HUVEC	blood vessel
7	chr7:38760600-38800200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr7:38761000-38820400	Weak transcription	Stomach Mucosa	stomach
9	chr7:38762600-38793200	Weak transcription	Hela-S3	cervix
10	chr7:38763200-38828000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:38763400-38792600	Weak transcription	Small Intestine	intestine
12	chr7:38763400-38828800	Weak transcription	HepG2	liver
13	chr7:38763800-38791600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr7:38765400-38802800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr7:38766000-38791800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr7:38766600-38791600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr7:38767200-38792600	Weak transcription	Colonic Mucosa	Colon
18	chr7:38767200-38802800	Weak transcription	Right Ventricle	heart
19	chr7:38767200-38805800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr7:38768400-38791200	Weak transcription	Brain Germinal Matrix	brain
21	chr7:38768400-38791800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr7:38769800-38795000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr7:38774800-38816800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr7:38775600-38791200	Weak transcription	HSMMtube	muscle
25	chr7:38775800-38816600	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr7:38776400-38792200	Weak transcription	Fetal Heart	heart
27	chr7:38777400-38800400	Strong transcription	Primary B cells from cord blood	blood
28	chr7:38779200-38792800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr7:38779800-38794800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:38780000-38792000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr7:38780800-38790200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr7:38780800-38792800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr7:38780800-38803600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr7:38780800-38806000	Weak transcription	Fetal Brain Female	brain
35	chr7:38780800-38828800	Weak transcription	Gastric	stomach
36	chr7:38781400-38790400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr7:38781400-38805800	Weak transcription	Brain Substantia Nigra	brain
38	chr7:38782000-38790200	Weak transcription	Brain Hippocampus Middle	brain
39	chr7:38782200-38791200	Weak transcription	K562	blood
40	chr7:38782600-38791400	Weak transcription	Brain Angular Gyrus	brain
41	chr7:38783000-38791400	Weak transcription	Colon Smooth Muscle	Colon
42	chr7:38783200-38790800	Weak transcription	Brain Anterior Caudate	brain
43	chr7:38783200-38791400	Weak transcription	Ovary	ovary
44	chr7:38784000-38791400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr7:38784400-38791200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr7:38784400-38805800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr7:38784600-38790800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr7:38784600-38805800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr7:38784800-38790800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr7:38784800-38790800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links