Variant report

Variant	rs1880696
Chromosome Location	chr12:119506064-119506065
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	chr12:119505058..119507410-chr12:119509441..119511568,2	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10744734	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10774483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10774485	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1525953	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1525954	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1525959	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1525971	0.92[EUR][1000 genomes]
rs2030829	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2091333	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs2393467	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3921268	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4354749	0.92[EUR][1000 genomes]
rs4429121	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4767761	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs6490223	0.92[TSI][hapmap]
rs7138083	0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs7298367	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7302780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7311043	0.92[EUR][1000 genomes]
rs7953473	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7980820	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][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	nsv1047036	chr12:119477583-119992640	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1880696	RAB35	cis	cerebellum	SCAN
rs1880696	TBX5	cis	cerebellum	SCAN
rs1880696	RPLP0	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:119499400-119506800	Weak transcription	Brain Germinal Matrix	brain
2	chr12:119505800-119506200	Enhancers	Fetal Brain Female	brain
3	chr12:119505800-119506600	Enhancers	Fetal Brain Male	brain
4	chr12:119505800-119506800	Enhancers	Pancreas	Pancrea
5	chr12:119505800-119507000	Enhancers	Right Ventricle	heart
6	chr12:119505800-119507200	Enhancers	Left Ventricle	heart
7	chr12:119505800-119507400	Enhancers	H1 Cell Line	embryonic stem cell
8	chr12:119505800-119507400	Enhancers	Fetal Muscle Leg	muscle
9	chr12:119505800-119507600	Enhancers	H9 Cell Line	embryonic stem cell
10	chr12:119505800-119510800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:119506000-119506400	Enhancers	Gastric	stomach
12	chr12:119506000-119506600	Enhancers	Lung	lung
13	chr12:119506000-119506800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:119506000-119507400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
15	chr12:119506000-119507600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
16	chr12:119506000-119510200	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links