Variant report

Variant	rs3774611
Chromosome Location	chr3:53840665-53840666
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11130381	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12485510	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2241807	0.89[CEU][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2241808	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2276838	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3774614	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7625247	0.92[CEU][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs7626693	0.81[CEU][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs877484	0.89[CEU][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs893365	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1003204	chr3:53820070-53877149	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1002375	chr3:53822319-53872753	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv876803	chr3:53822893-53889849	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv518466	chr3:53832903-53882663	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv521181	chr3:53833509-53881471	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	esv3437902	chr3:53837712-53842010	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3774611	ABHD14A	cis	parietal	SCAN
rs3774611	HEMK1	cis	cerebellum	SCAN
rs3774611	RBM6	cis	parietal	SCAN
rs3774611	PDE12	cis	parietal	SCAN
rs3774611	TLR9	cis	cerebellum	SCAN
rs3774611	IL17RB	Cis_1M	lymphoblastoid	RTeQTL
rs3774611	RFT1	cis	cerebellum	SCAN
rs3774611	CHDH	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53811600-53843600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:53829200-53853000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:53830400-53851200	Weak transcription	Fetal Brain Male	brain
4	chr3:53833600-53840800	Weak transcription	Fetal Kidney	kidney
5	chr3:53837600-53841800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:53838000-53841800	Enhancers	Fetal Thymus	thymus
7	chr3:53838200-53841200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:53838200-53841200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:53838200-53841200	Enhancers	NH-A	brain
10	chr3:53838200-53841400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:53838200-53841600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:53838200-53841600	Enhancers	Right Ventricle	heart
13	chr3:53838400-53841200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:53838400-53841200	Enhancers	A549	lung
15	chr3:53838400-53841200	Enhancers	NHLF	lung
16	chr3:53838400-53841400	Enhancers	HSMMtube	muscle
17	chr3:53838400-53842400	Enhancers	Fetal Heart	heart
18	chr3:53838600-53841000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:53838600-53841000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:53838600-53841200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr3:53839000-53840800	Weak transcription	Spleen	Spleen
22	chr3:53839000-53841600	Enhancers	NHDF-Ad	bronchial
23	chr3:53839000-53841800	Enhancers	GM12878-XiMat	blood
24	chr3:53839000-53849800	Strong transcription	Fetal Lung	lung
25	chr3:53839200-53855200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:53839400-53840800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:53839400-53851400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:53839600-53840800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr3:53839600-53841000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:53839600-53849000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr3:53839600-53851000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:53839600-53851200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:53839600-53852800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr3:53839600-53876600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:53839800-53843800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:53839800-53849200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:53840200-53840800	Enhancers	Brain Hippocampus Middle	brain
38	chr3:53840200-53841000	Enhancers	Placenta	Placenta
39	chr3:53840200-53841000	Flanking Active TSS	Osteobl	bone
40	chr3:53840200-53841200	Enhancers	Fetal Intestine Large	intestine
41	chr3:53840200-53841600	Enhancers	Brain Angular Gyrus	brain
42	chr3:53840200-53841600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:53840200-53841600	Enhancers	Left Ventricle	heart
44	chr3:53840200-53842200	Genic enhancers	Fetal Intestine Small	intestine
45	chr3:53840200-53842200	Enhancers	Pancreas	Pancrea
46	chr3:53840400-53841000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr3:53840400-53841000	Enhancers	Ovary	ovary
48	chr3:53840400-53841000	Enhancers	Stomach Smooth Muscle	stomach
49	chr3:53840400-53841200	Enhancers	Brain Anterior Caudate	brain
50	chr3:53840400-53841200	Enhancers	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links