Variant report

Variant	rs1031963
Chromosome Location	chr15:40451782-40451783
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	chr15:40401050..40404743-chr15:40451589..40454397,3	K562	blood:
2	chr15:40447852..40449370-chr15:40450050..40452943,2	K562	blood:
3	chr15:40332774..40337127-chr15:40449212..40452234,6	K562	blood:
4	chr15:40355705..40358626-chr15:40451633..40453971,2	K562	blood:
5	chr15:40334698..40337127-chr15:40449687..40452234,2	K562	blood:
6	chr15:40068522..40070743-chr15:40450771..40453010,2	K562	blood:
7	chr15:40399053..40404293-chr15:40451574..40455090,8	MCF-7	breast:
8	chr15:40447852..40449701-chr15:40449877..40452943,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000248508	Chromatin interaction
ENSG00000104081	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1031964	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518681	0.94[ASN][1000 genomes]
rs10518682	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11070253	0.96[ASN][1000 genomes]
rs11630664	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11631616	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632939	0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs11634065	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11636204	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11636293	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11637555	0.92[ASN][1000 genomes]
rs11854027	0.96[ASN][1000 genomes]
rs11854103	0.96[ASN][1000 genomes]
rs11854965	0.96[ASN][1000 genomes]
rs12898627	0.87[ASN][1000 genomes]
rs12898804	0.93[ASN][1000 genomes]
rs12899102	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12899779	0.87[ASN][1000 genomes]
rs12901947	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902191	0.94[ASN][1000 genomes]
rs12902458	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12903940	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12905742	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908093	0.96[ASN][1000 genomes]
rs12909888	0.93[ASN][1000 genomes]
rs12910199	0.91[ASN][1000 genomes]
rs12912902	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12912982	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12913620	0.84[ASN][1000 genomes]
rs12913741	0.84[ASN][1000 genomes]
rs12913803	0.84[ASN][1000 genomes]
rs12913994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12915249	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12916805	0.96[ASN][1000 genomes]
rs12916901	0.94[ASN][1000 genomes]
rs1471583	0.89[ASN][1000 genomes]
rs1565863	0.94[ASN][1000 genomes]
rs1565864	0.94[ASN][1000 genomes]
rs1565865	0.94[ASN][1000 genomes]
rs1565866	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16970409	0.96[ASN][1000 genomes]
rs1845477	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2002425	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2128013	0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2172742	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.93[ASN][1000 genomes]
rs2277560	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2290551	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.93[ASN][1000 genomes]
rs2305653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2412480	0.94[ASN][1000 genomes]
rs2898988	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34191615	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34358001	0.94[ASN][1000 genomes]
rs34823877	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3759839	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759842	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244573	0.93[ASN][1000 genomes]
rs4244574	0.94[ASN][1000 genomes]
rs4923856	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924419	0.86[ASN][1000 genomes]
rs4924420	0.83[ASN][1000 genomes]
rs4924422	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924424	0.94[ASN][1000 genomes]
rs4924425	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924427	0.97[ASN][1000 genomes]
rs4924428	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924429	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924430	0.97[ASN][1000 genomes]
rs62020024	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162894	0.93[ASN][1000 genomes]
rs7163546	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7164047	0.94[ASN][1000 genomes]
rs7164783	0.93[ASN][1000 genomes]
rs7169842	0.93[ASN][1000 genomes]
rs7170412	0.87[ASN][1000 genomes]
rs7180335	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.85[TSI][hapmap];0.92[ASN][1000 genomes]
rs7495483	0.93[ASN][1000 genomes]
rs8023395	0.90[ASN][1000 genomes]
rs8026738	0.97[ASN][1000 genomes]
rs8043080	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs876821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1031963	NUSAP1	cis	cerebellum	SCAN
rs1031963	DNAJC17	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40443200-40452800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr15:40447800-40452800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:40447800-40452800	Weak transcription	Right Atrium	heart
4	chr15:40448000-40452800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr15:40448000-40452800	Weak transcription	Fetal Intestine Large	intestine
6	chr15:40448200-40452600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:40448200-40452800	Weak transcription	Colonic Mucosa	Colon
8	chr15:40448200-40452800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:40448200-40452800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:40448400-40452400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:40448400-40452400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr15:40448400-40452600	Weak transcription	HMEC	breast
13	chr15:40448400-40452800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:40448400-40452800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr15:40448600-40452400	Weak transcription	Fetal Thymus	thymus
16	chr15:40448600-40452600	Weak transcription	Fetal Kidney	kidney
17	chr15:40448600-40452800	Weak transcription	Esophagus	oesophagus
18	chr15:40448600-40452800	Weak transcription	Fetal Lung	lung
19	chr15:40448600-40452800	Weak transcription	Gastric	stomach
20	chr15:40448600-40452800	Weak transcription	Lung	lung
21	chr15:40448600-40452800	Weak transcription	NHEK	skin
22	chr15:40448800-40452600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:40448800-40452600	Weak transcription	GM12878-XiMat	blood
24	chr15:40448800-40452800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr15:40448800-40452800	Weak transcription	Pancreas	Pancrea
26	chr15:40449200-40452600	Weak transcription	Stomach Mucosa	stomach
27	chr15:40449400-40452800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr15:40449400-40452800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr15:40449600-40452600	Enhancers	K562	blood
30	chr15:40449800-40452800	Weak transcription	Primary T cells from cord blood	blood
31	chr15:40450400-40451800	Enhancers	HepG2	liver
32	chr15:40450400-40452600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr15:40450400-40452600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr15:40450400-40452600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr15:40450400-40452600	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr15:40450400-40452800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr15:40450400-40452800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:40450600-40452600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:40450600-40452600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr15:40450600-40452600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr15:40450600-40452800	Weak transcription	Fetal Intestine Small	intestine
42	chr15:40450600-40453000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr15:40450800-40452600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:40450800-40452600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr15:40450800-40452600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr15:40450800-40452800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr15:40450800-40452800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr15:40450800-40452800	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr15:40450800-40453200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr15:40451000-40452200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links