Variant report

Variant	rs1248420
Chromosome Location	chr10:29281323-29281324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:29166106..29168504-chr10:29280590..29282791,2	K562	blood:
2	chr10:29279625..29282236-chr10:29283754..29288089,3	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10763679	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1248423	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1248424	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539248	0.83[EUR][1000 genomes]
rs1773879	0.83[EUR][1000 genomes]
rs2484510	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2783585	0.86[EUR][1000 genomes]
rs2783592	0.87[EUR][1000 genomes]
rs2795100	0.86[EUR][1000 genomes]
rs61838449	0.86[EUR][1000 genomes]
rs788051	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs805501	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1046678	chr10:29242479-29378871	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv540524	chr10:29242479-29378871	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:29273800-29290800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr10:29274600-29283200	Weak transcription	Aorta	Aorta
3	chr10:29279200-29281600	Enhancers	Placenta	Placenta
4	chr10:29279200-29281800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr10:29279400-29281600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr10:29279800-29281400	Enhancers	NHEK	skin
7	chr10:29279800-29281600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr10:29279800-29281800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr10:29280000-29281400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr10:29280000-29281400	Enhancers	Fetal Heart	heart
11	chr10:29280000-29281400	Enhancers	Hela-S3	cervix
12	chr10:29280000-29281400	Enhancers	HepG2	liver
13	chr10:29280000-29281400	Enhancers	HMEC	breast
14	chr10:29280000-29281400	Enhancers	HSMM	muscle
15	chr10:29280000-29281400	Enhancers	HSMMtube	muscle
16	chr10:29280000-29281600	Enhancers	Osteobl	bone
17	chr10:29280200-29281400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr10:29280200-29281600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr10:29280400-29281400	Flanking Active TSS	A549	lung
20	chr10:29280600-29281400	Enhancers	K562	blood
21	chr10:29280800-29281400	Enhancers	Lung	lung
22	chr10:29280800-29281400	Enhancers	NHLF	lung
23	chr10:29281000-29281400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr10:29281000-29281400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr10:29281000-29282800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr10:29281000-29285000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr10:29281200-29281400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr10:29281200-29281400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr10:29281200-29281400	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr10:29281200-29282800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:29281200-29285800	Weak transcription	NH-A	brain
32	chr10:29281200-29286200	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links