Variant report

Variant	rs2945152
Chromosome Location	chr1:85048641-85048642
allele	A/G
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:1)
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	chr1:85046450..85049039-chr1:85062565..85064761,2	K562	blood:
2	chr1:85039285..85040851-chr1:85047957..85050303,2	K562	blood:
3	chr1:85038924..85041180-chr1:85047534..85050087,3	K562	blood:
4	chr1:85035171..85039138-chr1:85044940..85048929,5	K562	blood:
5	chr1:84973183..84975597-chr1:85046521..85049495,2	K562	blood:
6	chr1:85047686..85049603-chr1:85052404..85054227,2	MCF-7	breast:
7	chr1:84967877..84970067-chr1:85047454..85049794,2	K562	blood:
8	chr1:84967877..84971482-chr1:85048294..85051877,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPF1-2	chr1:85047609-85049506	NONHSAT004219

No data

Variant related genes	Relation type
ENSG00000174021	Chromatin interaction
ENSG00000117151	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1144276	0.86[ASW][hapmap]
rs12128801	0.86[ASW][hapmap]
rs12403545	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs1246253	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs1246254	0.81[CHB][hapmap];0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs1400777	0.86[ASW][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1850508	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1850509	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2007454	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2303306	0.94[CHB][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs2303307	0.87[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs2911588	0.91[ASN][1000 genomes]
rs2911589	0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs2911590	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2911591	0.96[ASN][1000 genomes]
rs2911592	0.92[ASN][1000 genomes]
rs2911593	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2911595	0.83[CEU][hapmap];0.90[EUR][1000 genomes]
rs2911598	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2911599	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2911603	0.96[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2911604	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2911605	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2943663	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2943669	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2943670	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2943675	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2943676	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2943677	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2943678	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2945140	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2945142	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2945146	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2945148	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2945149	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2945150	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2945153	0.94[ASN][1000 genomes]
rs2945155	0.94[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2945158	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2945160	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2994937	0.85[ASN][1000 genomes]
rs2994940	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2994943	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2994944	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2994946	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2994947	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2994953	0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2994954	0.81[CHB][hapmap];0.91[CHD][hapmap]
rs3021402	0.81[CHB][hapmap];0.94[CHD][hapmap]
rs312397	0.86[ASW][hapmap]
rs41299545	0.98[ASN][1000 genomes]
rs6576713	0.93[ASW][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap]
rs6692765	0.86[CHB][hapmap];0.82[AMR][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	nsv1000325	chr1:85032605-85100748	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2945152	BCL10	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85040000-85049400	Weak transcription	Spleen	Spleen
2	chr1:85040800-85049200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:85041000-85048800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:85041000-85051600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:85041200-85049400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr1:85041400-85049200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:85043000-85050800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:85044200-85050800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr1:85045200-85048800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:85046800-85049200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:85047000-85048800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:85047200-85049200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:85047400-85049600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:85048200-85049600	Enhancers	Primary B cells from cord blood	blood
15	chr1:85048400-85049800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr1:85048400-85050000	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr1:85048400-85050400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr1:85048400-85050400	Enhancers	Primary B cells from peripheral blood	blood
19	chr1:85048400-85050400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:85048600-85048800	Enhancers	Gastric	stomach
21	chr1:85048600-85049200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:85048600-85049200	Bivalent/Poised TSS	HepG2	liver
23	chr1:85048600-85049400	Enhancers	Stomach Mucosa	stomach
24	chr1:85048600-85049400	Enhancers	NHDF-Ad	bronchial
25	chr1:85048600-85049600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:85048600-85049600	Enhancers	Right Atrium	heart
27	chr1:85048600-85049600	Flanking Active TSS	K562	blood
28	chr1:85048600-85050000	Enhancers	Fetal Brain Male	brain
29	chr1:85048600-85050000	Enhancers	Left Ventricle	heart
30	chr1:85048600-85050200	Enhancers	H1 Cell Line	embryonic stem cell
31	chr1:85048600-85050200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:85048600-85050200	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr1:85048600-85050200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:85048600-85050200	Enhancers	GM12878-XiMat	blood
35	chr1:85048600-85050400	Enhancers	Fetal Brain Female	brain

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