Variant report

Variant	rs57804899
Chromosome Location	chr3:196226547-196226548
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196221498..196224147-chr3:196224892..196227326,3	K562	blood:
2	chr3:196209119..196211761-chr3:196224016..196226759,2	K562	blood:
3	chr3:195954091..195957267-chr3:196224695..196228323,3	K562	blood:
4	chr3:196225951..196229671-chr3:196232919..196236791,4	K562	blood:

Variant related genes	Relation type
ENSG00000163959	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs55949784	1.00[AMR][1000 genomes]
rs56867889	1.00[AMR][1000 genomes]
rs57849945	1.00[AMR][1000 genomes]
rs59386010	1.00[AMR][1000 genomes]
rs73891240	1.00[AMR][1000 genomes]
rs73891248	1.00[AMR][1000 genomes]
rs73891254	1.00[AMR][1000 genomes]
rs73891256	1.00[AMR][1000 genomes]
rs73891257	1.00[AMR][1000 genomes]
rs73891262	1.00[AMR][1000 genomes]
rs73891265	1.00[AMR][1000 genomes]
rs73891267	1.00[AMR][1000 genomes]
rs73891269	1.00[AFR][1000 genomes];1.00[AMR][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	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv469831	chr3:196071603-196235225	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv482542	chr3:196071603-196235225	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	esv2752687	chr3:196147690-196286690	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
9	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
10	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196199400-196227000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:196213000-196226800	Weak transcription	Fetal Kidney	kidney
3	chr3:196213800-196226600	Weak transcription	Brain Substantia Nigra	brain
4	chr3:196214400-196226600	Weak transcription	Aorta	Aorta
5	chr3:196214400-196226800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:196214400-196226800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:196214400-196226800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:196214400-196226800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:196214400-196226800	Weak transcription	Brain Anterior Caudate	brain
10	chr3:196214400-196226800	Weak transcription	Pancreas	Pancrea
11	chr3:196214400-196227000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:196214400-196227000	Weak transcription	Fetal Lung	lung
13	chr3:196214400-196227000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:196214400-196228200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:196214600-196226800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:196214600-196226800	Weak transcription	Colonic Mucosa	Colon
17	chr3:196214600-196226800	Weak transcription	Fetal Intestine Large	intestine
18	chr3:196214600-196226800	Weak transcription	Lung	lung
19	chr3:196214800-196227200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:196215000-196227000	Weak transcription	Placenta	Placenta
21	chr3:196215800-196226800	Weak transcription	Right Atrium	heart
22	chr3:196217600-196226800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:196217800-196226800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:196217800-196227000	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:196218000-196227000	Weak transcription	Brain Angular Gyrus	brain
26	chr3:196221200-196226600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr3:196223400-196226800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:196223400-196226800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr3:196223400-196226800	Weak transcription	NHLF	lung
30	chr3:196223400-196227000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:196223600-196226800	Weak transcription	Primary B cells from peripheral blood	blood
32	chr3:196223800-196226600	Weak transcription	Primary T cells from cord blood	blood
33	chr3:196223800-196226600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:196223800-196226600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr3:196223800-196226800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:196223800-196226800	Weak transcription	Primary B cells from cord blood	blood
37	chr3:196223800-196226800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:196223800-196226800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:196223800-196227000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr3:196224600-196226600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:196224600-196226800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:196224600-196226800	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr3:196224600-196226800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:196224800-196226600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr3:196224800-196227400	Transcr. at gene 5' and 3'	Dnd41	blood
46	chr3:196225000-196227200	Genic enhancers	Primary T cells fromperipheralblood	blood
47	chr3:196225000-196227200	Enhancers	Left Ventricle	heart
48	chr3:196225000-196227200	Enhancers	Ovary	ovary
49	chr3:196225000-196227600	Enhancers	Small Intestine	intestine
50	chr3:196225200-196226800	Genic enhancers	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links