Variant report

Variant	rs1890950
Chromosome Location	chr10:23113841-23113842
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	chr10:23112958..23115115-chr10:23343406..23346225,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10764345	0.97[ASN][1000 genomes]
rs10828337	0.90[ASN][1000 genomes]
rs10828342	0.90[ASN][1000 genomes]
rs10828343	0.90[ASN][1000 genomes]
rs11013139	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11013141	0.87[ASN][1000 genomes]
rs11013146	0.93[ASN][1000 genomes]
rs11492538	0.91[ASN][1000 genomes]
rs1417374	0.81[ASN][1000 genomes]
rs1538887	0.90[ASN][1000 genomes]
rs4534468	0.87[EUR][1000 genomes]
rs4747447	0.90[ASN][1000 genomes]
rs4748821	0.86[ASN][1000 genomes]
rs4748822	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs4748823	0.80[ASW][hapmap];0.90[YRI][hapmap]
rs7068009	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7085974	0.90[EUR][1000 genomes]
rs7093389	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7098985	0.90[YRI][hapmap]
rs73600525	0.88[ASN][1000 genomes]
rs7898655	0.91[ASN][1000 genomes]
rs9732527	0.90[ASN][1000 genomes]
rs9732534	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894960	chr10:23049139-23113841	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv894961	chr10:23049139-23128475	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv894962	chr10:23050683-23113841	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv894963	chr10:23050683-23121820	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv894964	chr10:23050683-23128475	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv894965	chr10:23071128-23113841	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv2764013	chr10:23087298-23239345	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv894966	chr10:23090535-23202522	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1890950	PTF1A	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:23100200-23114400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr10:23109800-23115200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr10:23110000-23114800	Enhancers	HUVEC	blood vessel
4	chr10:23110200-23114200	Enhancers	NHDF-Ad	bronchial
5	chr10:23110200-23114600	Enhancers	NH-A	brain
6	chr10:23110800-23114000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr10:23111400-23114200	Enhancers	NHLF	lung
8	chr10:23111800-23114400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr10:23111800-23114400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr10:23111800-23114600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr10:23111800-23114800	Enhancers	HepG2	liver
12	chr10:23111800-23114800	Enhancers	HSMM	muscle
13	chr10:23111800-23115200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr10:23111800-23115400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr10:23111800-23115400	Enhancers	HMEC	breast
16	chr10:23112000-23115200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr10:23112400-23120600	Weak transcription	HSMMtube	muscle
18	chr10:23112600-23115200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr10:23112800-23114400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr10:23112800-23115200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr10:23113200-23114000	Enhancers	Esophagus	oesophagus
22	chr10:23113200-23114400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr10:23113200-23115000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr10:23113400-23115000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr10:23113600-23114600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr10:23113800-23114000	Enhancers	A549	lung
27	chr10:23113800-23114200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr10:23113800-23114200	Flanking Active TSS	NHEK	skin
29	chr10:23113800-23114200	Flanking Active TSS	Osteobl	bone
30	chr10:23113800-23114600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr10:23113800-23116000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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