Variant report

Variant	rs10841551
Chromosome Location	chr12:20640164-20640165
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	chr12:20638848..20641263-chr12:20644275..20646310,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10841550	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045256	0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs11045257	0.83[EUR][1000 genomes]
rs11045279	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12184495	0.82[EUR][1000 genomes]
rs12372360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12815826	0.82[EUR][1000 genomes]
rs4130514	0.82[EUR][1000 genomes]
rs7302508	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7484431	0.83[EUR][1000 genomes]
rs7978217	0.95[CEU][hapmap];0.84[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	nsv1048067	chr12:20363755-20874845	Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv541408	chr12:20363755-20874845	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1046870	chr12:20509914-20711535	Active TSS Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	nsv541409	chr12:20509914-20711535	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
5	nsv557701	chr12:20614024-20643574	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10841551	PHYHD1	trans	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20607800-20645000	Weak transcription	Right Ventricle	heart
2	chr12:20619200-20654200	Weak transcription	Fetal Stomach	stomach
3	chr12:20628600-20644400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:20629200-20640200	Weak transcription	NHLF	lung
5	chr12:20631600-20640200	Weak transcription	Aorta	Aorta
6	chr12:20632800-20647200	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:20635200-20641000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:20635200-20641400	Enhancers	NHDF-Ad	bronchial
9	chr12:20635800-20641000	Weak transcription	Fetal Intestine Large	intestine
10	chr12:20636400-20641400	Weak transcription	Fetal Intestine Small	intestine
11	chr12:20636400-20641400	Weak transcription	Left Ventricle	heart
12	chr12:20637000-20642800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:20637200-20643200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:20638600-20642600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr12:20639000-20640400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr12:20639200-20640400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:20639200-20640400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:20639200-20640400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:20639200-20640600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:20639400-20640200	Enhancers	HUVEC	blood vessel
21	chr12:20639400-20641600	Enhancers	Osteobl	bone
22	chr12:20639400-20643000	Enhancers	A549	lung
23	chr12:20639600-20640600	Weak transcription	Hela-S3	cervix
24	chr12:20639600-20641000	Weak transcription	Brain Substantia Nigra	brain
25	chr12:20639800-20640400	Weak transcription	Psoas Muscle	Psoas
26	chr12:20639800-20645200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:20639800-20645200	Weak transcription	Right Atrium	heart
28	chr12:20639800-20648200	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links