Variant report

Variant	rs3857079
Chromosome Location	chr4:149094468-149094469
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11099680	0.90[ASN][1000 genomes]
rs11099681	0.83[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs3843410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3843411	0.87[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs3843413	0.82[CHB][hapmap]
rs4835491	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4835493	0.87[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs4835503	0.82[CHB][hapmap]
rs4835504	0.83[CHB][hapmap]
rs4835506	0.85[CHB][hapmap]
rs6535584	0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs6535590	0.82[CHB][hapmap]
rs6535593	0.82[CHB][hapmap]
rs6535594	0.82[CHB][hapmap]
rs6828665	0.82[CHB][hapmap]
rs6844155	0.93[CHB][hapmap]
rs6846591	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs6848375	0.81[ASW][hapmap];0.95[YRI][hapmap]
rs7694064	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032794	chr4:149046598-149135489	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv537295	chr4:149046598-149135489	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3857079	TTC29	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:149045600-149104800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr4:149068000-149097400	Weak transcription	Spleen	Spleen
3	chr4:149076000-149094600	Weak transcription	Fetal Stomach	stomach
4	chr4:149084000-149106200	Weak transcription	Lung	lung
5	chr4:149086200-149095000	Weak transcription	Stomach Mucosa	stomach
6	chr4:149087600-149123400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:149088000-149113200	Weak transcription	Adipose Nuclei	Adipose
8	chr4:149088000-149113600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:149088400-149113000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr4:149088400-149122800	Weak transcription	Brain Angular Gyrus	brain
11	chr4:149089200-149095400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr4:149092400-149113400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:149093000-149095000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr4:149093000-149095800	Weak transcription	Colonic Mucosa	Colon
15	chr4:149093000-149102000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr4:149093000-149102000	Weak transcription	Left Ventricle	heart
17	chr4:149094200-149094600	Enhancers	Small Intestine	intestine
18	chr4:149094200-149094800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:149094200-149096000	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr4:149094400-149094600	Enhancers	Brain Hippocampus Middle	brain
21	chr4:149094400-149094600	Enhancers	Pancreas	Pancrea
22	chr4:149094400-149095400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:149094400-149113200	Weak transcription	Rectal Mucosa Donor 29	rectum

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