Variant report

Variant	rs12903940
Chromosome Location	chr15:40449993-40449994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr15:40449979-40450556	HL-60	blood:	n/a	chr15:40450206-40450213 chr15:40450203-40450216
2	SPI1	chr15:40449964-40450449	HL-60	blood:	n/a	chr15:40450206-40450213 chr15:40450203-40450216

No.	Distal block	Cell Line	Cell type
1	chr15:40407953..40409735-chr15:40448787..40451780,2	K562	blood:
2	chr15:40332774..40337127-chr15:40449212..40452234,6	K562	blood:
3	chr15:40448813..40450482-chr15:40453817..40455568,2	K562	blood:
4	chr15:40334698..40337127-chr15:40449687..40452234,2	K562	blood:
5	chr15:40447852..40449701-chr15:40449877..40452943,3	K562	blood:

Variant related genes	Relation type
BUB1B	TF binding region

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1031963	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1031964	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10518681	0.91[ASN][1000 genomes]
rs10518682	0.91[ASN][1000 genomes]
rs11070253	0.92[ASN][1000 genomes]
rs11630664	0.93[ASN][1000 genomes]
rs11631616	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11632939	0.89[ASN][1000 genomes]
rs11634065	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11636204	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11636293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11637555	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11854027	0.93[ASN][1000 genomes]
rs11854103	0.93[ASN][1000 genomes]
rs11854965	0.93[ASN][1000 genomes]
rs12898627	0.90[ASN][1000 genomes]
rs12898804	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12899102	0.93[ASN][1000 genomes]
rs12899779	0.90[ASN][1000 genomes]
rs12901947	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12902191	0.91[ASN][1000 genomes]
rs12902458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905742	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12908093	0.93[ASN][1000 genomes]
rs12909888	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12910199	0.94[ASN][1000 genomes]
rs12912902	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912982	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12913620	0.88[ASN][1000 genomes]
rs12913741	0.88[ASN][1000 genomes]
rs12913803	0.88[ASN][1000 genomes]
rs12913994	0.92[ASN][1000 genomes]
rs12915249	0.89[ASN][1000 genomes]
rs12916805	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12916901	0.91[ASN][1000 genomes]
rs1471583	0.92[ASN][1000 genomes]
rs1565863	0.91[ASN][1000 genomes]
rs1565864	0.91[ASN][1000 genomes]
rs1565865	0.91[ASN][1000 genomes]
rs1565866	0.97[ASN][1000 genomes]
rs16970409	0.93[ASN][1000 genomes]
rs1845477	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002425	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2128013	0.89[ASN][1000 genomes]
rs2172742	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2277560	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290551	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2305653	0.93[ASN][1000 genomes]
rs2412480	0.91[ASN][1000 genomes]
rs2898988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34191615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34358001	0.91[ASN][1000 genomes]
rs34823877	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3759839	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3759842	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4244573	0.90[ASN][1000 genomes]
rs4244574	0.91[ASN][1000 genomes]
rs4923856	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4924419	0.83[ASN][1000 genomes]
rs4924420	0.86[ASN][1000 genomes]
rs4924422	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924424	0.91[ASN][1000 genomes]
rs4924425	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924427	0.93[ASN][1000 genomes]
rs4924428	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924429	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4924430	0.94[ASN][1000 genomes]
rs62020024	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7162894	0.89[ASN][1000 genomes]
rs7163546	0.91[ASN][1000 genomes]
rs7164047	0.91[ASN][1000 genomes]
rs7164783	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7169842	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7170412	0.84[ASN][1000 genomes]
rs7180335	0.96[ASN][1000 genomes]
rs7495483	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8023395	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8026738	0.93[ASN][1000 genomes]
rs8043080	0.97[ASN][1000 genomes]
rs876821	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40443200-40452800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr15:40446800-40450400	Enhancers	H9 Cell Line	embryonic stem cell
3	chr15:40447800-40451000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:40447800-40452800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:40447800-40452800	Weak transcription	Right Atrium	heart
6	chr15:40448000-40450000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:40448000-40450000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:40448000-40450800	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr15:40448000-40452800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr15:40448000-40452800	Weak transcription	Fetal Intestine Large	intestine
11	chr15:40448200-40452600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:40448200-40452800	Weak transcription	Colonic Mucosa	Colon
13	chr15:40448200-40452800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr15:40448200-40452800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr15:40448400-40450000	Weak transcription	Fetal Intestine Small	intestine
16	chr15:40448400-40452400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:40448400-40452400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr15:40448400-40452600	Weak transcription	HMEC	breast
19	chr15:40448400-40452800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr15:40448400-40452800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr15:40448600-40450400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr15:40448600-40450600	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr15:40448600-40452400	Weak transcription	Fetal Thymus	thymus
24	chr15:40448600-40452600	Weak transcription	Fetal Kidney	kidney
25	chr15:40448600-40452800	Weak transcription	Esophagus	oesophagus
26	chr15:40448600-40452800	Weak transcription	Fetal Lung	lung
27	chr15:40448600-40452800	Weak transcription	Gastric	stomach
28	chr15:40448600-40452800	Weak transcription	Lung	lung
29	chr15:40448600-40452800	Weak transcription	NHEK	skin
30	chr15:40448800-40450000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr15:40448800-40450400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr15:40448800-40452600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:40448800-40452600	Weak transcription	GM12878-XiMat	blood
34	chr15:40448800-40452800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:40448800-40452800	Weak transcription	Pancreas	Pancrea
36	chr15:40449000-40450600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr15:40449200-40452600	Weak transcription	Stomach Mucosa	stomach
38	chr15:40449400-40452800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr15:40449400-40452800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr15:40449600-40450200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr15:40449600-40452600	Enhancers	K562	blood
42	chr15:40449800-40450000	Enhancers	HepG2	liver
43	chr15:40449800-40450600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr15:40449800-40450800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:40449800-40450800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:40449800-40450800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr15:40449800-40450800	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr15:40449800-40451000	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr15:40449800-40451000	Enhancers	Placenta	Placenta
50	chr15:40449800-40452800	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links