Variant report

Variant	rs1435573
Chromosome Location	chr2:178936373-178936374
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:178934356..178936456-chr2:179417127..179418784,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10497482	0.93[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap]
rs11686720	0.93[ASW][hapmap];0.89[MKK][hapmap];0.87[YRI][hapmap]
rs12613904	0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs12987515	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs12994400	0.80[EUR][1000 genomes]
rs12994494	0.93[CEU][hapmap]
rs13002118	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs13002245	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs13002444	0.93[CEU][hapmap]
rs13004202	0.93[CEU][hapmap]
rs13006992	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs13007409	0.99[EUR][1000 genomes]
rs13007766	0.81[CEU][hapmap]
rs13010041	0.93[CEU][hapmap]
rs13012088	0.93[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap]
rs13014945	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs13019139	0.99[EUR][1000 genomes]
rs13030321	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1369518	0.93[ASW][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs1435574	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs17329811	0.93[CEU][hapmap]
rs2117739	0.93[ASW][hapmap];0.92[MKK][hapmap]
rs2164330	0.87[YRI][hapmap]
rs2366352	0.87[YRI][hapmap]
rs2886651	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs2886653	0.93[ASW][hapmap];0.92[MKK][hapmap];0.87[YRI][hapmap]
rs34261053	0.97[EUR][1000 genomes]
rs34595897	0.84[EUR][1000 genomes]
rs34648335	0.84[EUR][1000 genomes]
rs34699522	0.84[EUR][1000 genomes]
rs35068650	0.99[EUR][1000 genomes]
rs35397469	0.98[EUR][1000 genomes]
rs35678669	0.84[EUR][1000 genomes]
rs35691613	0.94[EUR][1000 genomes]
rs35862134	0.84[EUR][1000 genomes]
rs35987785	0.84[EUR][1000 genomes]
rs6746482	1.00[CEU][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71423525	0.84[EUR][1000 genomes]
rs71423542	0.97[EUR][1000 genomes]
rs71423543	0.95[EUR][1000 genomes]
rs71423544	0.97[EUR][1000 genomes]
rs7574975	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs7588301	0.86[CEU][hapmap]
rs920095	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs9288012	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs9288013	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs959775	0.93[ASW][hapmap];0.92[MKK][hapmap];0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533377	chr2:178718801-178963463	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv875451	chr2:178748294-178953409	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1435573	CHRNA1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178931600-178937000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:178932000-178936600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:178934200-178937000	Enhancers	Liver	Liver
4	chr2:178935600-178936600	Enhancers	Duodenum Mucosa	Duodenum
5	chr2:178935600-178937000	Enhancers	Fetal Intestine Small	intestine
6	chr2:178935600-178937000	Enhancers	Rectal Mucosa Donor 29	rectum
7	chr2:178935600-178937000	Weak transcription	Stomach Mucosa	stomach
8	chr2:178935600-178937400	Flanking Active TSS	K562	blood
9	chr2:178935800-178937000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:178935800-178937000	Enhancers	Fetal Intestine Large	intestine
11	chr2:178935800-178937000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:178936200-178937200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:178936200-178937200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:178936200-178937200	Flanking Active TSS	Pancreas	Pancrea
15	chr2:178936200-178937200	Enhancers	Right Ventricle	heart
16	chr2:178936200-178937400	Flanking Bivalent TSS/Enh	HepG2	liver
17	chr2:178936200-178938000	Active TSS	A549	lung

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