Variant report

Variant	rs1109497
Chromosome Location	chr3:47059944-47059945
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46985961..46989571-chr3:47058662..47060411,3	K562	blood:
2	chr3:47051592..47055905-chr3:47059567..47061970,4	K562	blood:

Variant related genes	Relation type
ENSG00000236409	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10510753	0.89[AMR][1000 genomes]
rs17079331	0.89[AMR][1000 genomes]
rs17079336	1.00[AMR][1000 genomes]
rs2385870	0.89[AMR][1000 genomes]
rs4515087	0.89[AMR][1000 genomes]
rs57246717	0.89[AMR][1000 genomes]
rs57313197	0.89[AMR][1000 genomes]
rs58906143	0.89[AMR][1000 genomes]
rs60579303	0.89[AMR][1000 genomes]
rs60811415	1.00[AMR][1000 genomes]
rs60949675	0.89[AMR][1000 genomes]
rs6442058	0.89[AMR][1000 genomes]
rs6768374	0.89[AMR][1000 genomes]
rs6772269	0.89[AMR][1000 genomes]
rs6809110	0.89[AMR][1000 genomes]
rs72895783	0.89[AMR][1000 genomes]
rs72905877	0.89[AMR][1000 genomes]
rs72905900	0.89[AMR][1000 genomes]
rs72907932	0.89[AMR][1000 genomes]
rs72913641	0.87[AMR][1000 genomes]
rs72913651	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs72913679	0.89[AMR][1000 genomes]
rs7612808	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv997261	chr3:47054766-47133680	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47050200-47063800	Weak transcription	Stomach Mucosa	stomach
2	chr3:47051400-47064000	Weak transcription	Small Intestine	intestine
3	chr3:47051800-47060400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:47051800-47061600	Weak transcription	Right Atrium	heart
5	chr3:47051800-47062000	Weak transcription	Psoas Muscle	Psoas
6	chr3:47052000-47062200	Strong transcription	Fetal Stomach	stomach
7	chr3:47052400-47061200	Strong transcription	Spleen	Spleen
8	chr3:47053200-47062400	Strong transcription	Fetal Muscle Trunk	muscle
9	chr3:47053400-47062200	Strong transcription	Fetal Muscle Leg	muscle
10	chr3:47054000-47061800	Strong transcription	Placenta	Placenta
11	chr3:47054200-47061600	Genic enhancers	Fetal Intestine Small	intestine
12	chr3:47054200-47062400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:47054400-47061400	Strong transcription	Stomach Smooth Muscle	stomach
14	chr3:47054400-47062000	Strong transcription	Adipose Nuclei	Adipose
15	chr3:47054600-47062800	Strong transcription	Fetal Brain Female	brain
16	chr3:47054800-47060600	Weak transcription	Fetal Heart	heart
17	chr3:47054800-47060800	Weak transcription	Fetal Brain Male	brain
18	chr3:47055000-47061600	Strong transcription	Brain Hippocampus Middle	brain
19	chr3:47055000-47062000	Strong transcription	Brain Cingulate Gyrus	brain
20	chr3:47055000-47062400	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:47055200-47061400	Genic enhancers	Fetal Thymus	thymus
22	chr3:47055400-47061800	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr3:47055400-47062200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:47055400-47063000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:47055600-47061600	Strong transcription	Left Ventricle	heart
26	chr3:47055600-47061800	Strong transcription	Brain Angular Gyrus	brain
27	chr3:47055600-47062000	Strong transcription	Brain Substantia Nigra	brain
28	chr3:47055600-47062000	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr3:47056400-47061800	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:47056600-47062200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:47056800-47061000	Strong transcription	Rectal Smooth Muscle	rectum
32	chr3:47056800-47061200	Genic enhancers	Fetal Intestine Large	intestine
33	chr3:47056800-47061800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:47056800-47062000	Strong transcription	Fetal Lung	lung
35	chr3:47056800-47062400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:47057000-47061000	Strong transcription	Colon Smooth Muscle	Colon
37	chr3:47057000-47061200	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:47057200-47066600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:47057400-47061200	Strong transcription	Right Ventricle	heart
40	chr3:47057600-47060000	Genic enhancers	Muscle Satellite Cultured Cells	--
41	chr3:47057600-47060200	Genic enhancers	HUES64 Cell Line	embryonic stem cell
42	chr3:47057600-47060600	Genic enhancers	NH-A	brain
43	chr3:47057600-47060800	Genic enhancers	Thymus	Thymus
44	chr3:47057600-47061200	Genic enhancers	Primary B cells from peripheral blood	blood
45	chr3:47057600-47061400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:47057800-47060600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr3:47057800-47061400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:47057800-47062200	Strong transcription	Aorta	Aorta
49	chr3:47057800-47062200	Strong transcription	Fetal Kidney	kidney
50	chr3:47058000-47060000	Genic enhancers	Primary T helper cells fromperipheralblood	blood

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