Variant report

Variant	rs6828945
Chromosome Location	chr4:121767758-121767759
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10857073	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10857074	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1397767	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes]
rs2102551	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2251270	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597553	0.85[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667170	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2667192	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3114953	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs343173	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs343176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs343177	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343183	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs343191	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4833673	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6846000	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs843557	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs907295	0.81[EUR][1000 genomes]
rs9991423	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879852	chr4:121108734-121768496	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1013704	chr4:121657648-121791601	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6828945	SYNPO2	cis	parietal	SCAN
rs6828945	QRFPR	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:121729600-121770400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr4:121750400-121768400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr4:121755800-121774600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr4:121756800-121779800	Weak transcription	Aorta	Aorta
5	chr4:121758200-121770400	Weak transcription	HSMM	muscle
6	chr4:121758200-121774600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:121759600-121775400	Weak transcription	Gastric	stomach
8	chr4:121760400-121775800	Weak transcription	Lung	lung
9	chr4:121761200-121778200	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:121761200-121783600	Weak transcription	Pancreas	Pancrea
11	chr4:121761400-121774600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:121761400-121777600	Weak transcription	Left Ventricle	heart
13	chr4:121763400-121778800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr4:121763600-121776600	Weak transcription	Fetal Stomach	stomach
15	chr4:121763800-121769800	Weak transcription	Osteobl	bone
16	chr4:121763800-121770400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:121763800-121771000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:121763800-121776600	Weak transcription	Fetal Heart	heart
19	chr4:121764000-121770000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:121764200-121767800	Weak transcription	Colon Smooth Muscle	Colon
21	chr4:121764400-121769600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:121765800-121786600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:121766000-121776600	Weak transcription	Fetal Intestine Small	intestine
24	chr4:121766000-121786600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr4:121766200-121769600	Weak transcription	NHDF-Ad	bronchial
26	chr4:121766200-121790800	Weak transcription	Ovary	ovary
27	chr4:121766400-121769400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:121766400-121776600	Weak transcription	Fetal Intestine Large	intestine
29	chr4:121766800-121768000	Weak transcription	Fetal Lung	lung
30	chr4:121767400-121769000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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