Variant report

Variant	rs7178873
Chromosome Location	chr15:40489387-40489388
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	chr15:40079175..40081149-chr15:40487705..40489916,2	K562	blood:
2	chr15:40487922..40490370-chr15:40496350..40498700,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11070254	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070255	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12102172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12385956	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13380113	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13380241	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1494533	0.80[YRI][hapmap]
rs1494534	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1801528	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1869906	1.00[EUR][1000 genomes]
rs28390245	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28417868	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28485685	1.00[EUR][1000 genomes]
rs28501335	1.00[EUR][1000 genomes]
rs28526743	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28561898	1.00[EUR][1000 genomes]
rs28565228	1.00[EUR][1000 genomes]
rs28606396	1.00[EUR][1000 genomes]
rs28637656	1.00[EUR][1000 genomes]
rs28637697	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28657938	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28668026	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28673302	1.00[EUR][1000 genomes]
rs28744626	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28750294	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28792493	1.00[EUR][1000 genomes]
rs28844897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28869227	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35611758	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55984256	1.00[EUR][1000 genomes]
rs56010221	1.00[EUR][1000 genomes]
rs56888636	1.00[EUR][1000 genomes]
rs57029027	1.00[EUR][1000 genomes]
rs58216655	1.00[EUR][1000 genomes]
rs58584688	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58870954	1.00[EUR][1000 genomes]
rs60743501	1.00[EUR][1000 genomes]
rs60889301	1.00[EUR][1000 genomes]
rs61579851	1.00[EUR][1000 genomes]
rs61678895	1.00[EUR][1000 genomes]
rs6492943	1.00[EUR][1000 genomes]
rs7164281	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7168394	1.00[EUR][1000 genomes]
rs7168416	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7173239	1.00[EUR][1000 genomes]
rs7175153	1.00[EUR][1000 genomes]
rs73377835	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383123	1.00[EUR][1000 genomes]
rs73389487	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389489	1.00[EUR][1000 genomes]
rs73389492	1.00[EUR][1000 genomes]
rs73389507	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389520	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389531	1.00[EUR][1000 genomes]
rs73389536	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389540	1.00[EUR][1000 genomes]
rs73390146	1.00[EUR][1000 genomes]
rs73390155	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390167	1.00[EUR][1000 genomes]
rs73390168	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390187	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73392641	1.00[EUR][1000 genomes]
rs8023956	1.00[EUR][1000 genomes]
rs8026988	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8364	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9672591	1.00[EUR][1000 genomes]
rs9806126	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9806144	0.89[AMR][1000 genomes];1.00[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	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7178873	BUB1B	cis	multi-tissue	Pritchard

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40453800-40525000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:40454000-40515200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:40454600-40502400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr15:40454800-40524200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:40455400-40530400	Weak transcription	Fetal Brain Female	brain
6	chr15:40455600-40518200	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:40455600-40522200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:40455600-40530400	Weak transcription	Brain Germinal Matrix	brain
9	chr15:40456200-40524000	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr15:40456200-40524000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:40464000-40490200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr15:40465000-40489600	Weak transcription	Fetal Intestine Large	intestine
13	chr15:40471400-40517600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:40471400-40524400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:40473200-40517800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr15:40473600-40525200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:40475000-40491600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr15:40475000-40526400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr15:40475400-40522600	Strong transcription	Dnd41	blood
20	chr15:40475600-40490000	Strong transcription	Fetal Thymus	thymus
21	chr15:40476200-40489400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:40476600-40490000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr15:40476800-40491600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr15:40478000-40489600	Weak transcription	Primary B cells from cord blood	blood
25	chr15:40479400-40492200	Weak transcription	Fetal Kidney	kidney
26	chr15:40480600-40500000	Weak transcription	Fetal Intestine Small	intestine
27	chr15:40481800-40524400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:40482200-40492400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr15:40482800-40497000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr15:40483000-40526200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr15:40483200-40501000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:40483400-40490200	Weak transcription	NHEK	skin
33	chr15:40483400-40490800	Weak transcription	Thymus	Thymus
34	chr15:40483800-40493000	Strong transcription	K562	blood
35	chr15:40483800-40509400	Weak transcription	Fetal Brain Male	brain
36	chr15:40484000-40490000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr15:40484400-40497800	Weak transcription	Osteobl	bone
38	chr15:40485200-40494400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr15:40485400-40489800	Weak transcription	Fetal Muscle Leg	muscle
40	chr15:40485400-40490200	Weak transcription	Fetal Stomach	stomach
41	chr15:40485400-40496200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:40485400-40513800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr15:40485400-40527600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:40485600-40492800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr15:40486600-40521000	Weak transcription	Placenta	Placenta
46	chr15:40486800-40489800	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr15:40486800-40490600	Weak transcription	HUVEC	blood vessel
48	chr15:40487200-40489600	Weak transcription	Hela-S3	cervix
49	chr15:40487600-40490000	Strong transcription	Fetal Lung	lung
50	chr15:40487600-40518200	Strong transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links