Variant report

Variant	rs1171050
Chromosome Location	chr1:190446253-190446254
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10494634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1171023	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1171032	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1171048	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1697590	0.84[JPT][hapmap];0.82[MEX][hapmap]
rs1697593	0.84[ASN][1000 genomes]
rs17369061	0.85[LWK][hapmap]
rs2455085	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932040	chr1:190005334-190914580	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv872758	chr1:190351677-190510003	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv872760	chr1:190377988-190577336	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872761	chr1:190389741-190485034	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv872762	chr1:190389741-190510003	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv872763	chr1:190389741-190531642	Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv872764	chr1:190399946-190531642	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv872765	chr1:190418653-190464647	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv466750	chr1:190433413-190496007	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv548551	chr1:190433413-190496007	Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv466761	chr1:190433413-190545283	Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv548552	chr1:190433413-190545283	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv466772	chr1:190446253-190492280	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv548553	chr1:190446253-190492280	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1171050	PPA1	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:190440000-190448800	Active TSS	Duodenum Mucosa	Duodenum
2	chr1:190440200-190448800	Active TSS	Fetal Intestine Large	intestine
3	chr1:190440800-190448600	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr1:190440800-190448800	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr1:190441200-190448600	Active TSS	Fetal Intestine Small	intestine
6	chr1:190441200-190448600	Active TSS	Right Atrium	heart
7	chr1:190443000-190449600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:190444800-190447200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
9	chr1:190445000-190446600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
10	chr1:190445000-190447600	Active TSS	Brain Angular Gyrus	brain
11	chr1:190445200-190447200	Weak transcription	Gastric	stomach
12	chr1:190445200-190449000	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr1:190445400-190446600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:190445400-190446800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:190445400-190446800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:190445400-190446800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:190445400-190446800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:190445400-190447200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:190445400-190447200	Weak transcription	Pancreas	Pancrea
20	chr1:190445400-190447200	Weak transcription	NHLF	lung
21	chr1:190445600-190446600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
22	chr1:190445600-190446600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
23	chr1:190445600-190446600	Weak transcription	Colonic Mucosa	Colon
24	chr1:190445600-190446800	Active TSS	Fetal Brain Female	brain
25	chr1:190445600-190447000	Weak transcription	Right Ventricle	heart
26	chr1:190445800-190446600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
27	chr1:190445800-190446600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:190445800-190446600	Weak transcription	Fetal Stomach	stomach
29	chr1:190445800-190446800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:190446000-190446600	Enhancers	Fetal Brain Male	brain
31	chr1:190446000-190446800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr1:190446200-190446600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
33	chr1:190446200-190448800	Active TSS	Brain Germinal Matrix	brain
34	chr1:190446200-190449600	Active TSS	Brain Anterior Caudate	brain
35	chr1:190446200-190450000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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