Variant report

Variant	rs56898787
Chromosome Location	chr3:52436259-52436260
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52420073..52422449-chr3:52434521..52436360,2	K562	blood:
2	chr3:52320927..52323255-chr3:52435150..52437326,2	K562	blood:
3	chr3:52435154..52438907-chr3:52439834..52442973,4	MCF-7	breast:
4	chr3:52435594..52437407-chr3:52437551..52439169,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168237	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000163930	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs3890123	1.00[AMR][1000 genomes]
rs55971019	1.00[AMR][1000 genomes]
rs56961704	1.00[AMR][1000 genomes]
rs58781613	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59528332	1.00[EUR][1000 genomes]
rs60499166	1.00[AMR][1000 genomes]
rs60997031	1.00[AMR][1000 genomes]
rs61734628	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61737029	1.00[EUR][1000 genomes]
rs6766038	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965257	1.00[EUR][1000 genomes]
rs73835766	1.00[AMR][1000 genomes]
rs73837049	1.00[AMR][1000 genomes]
rs73837599	1.00[AMR][1000 genomes]
rs73838354	1.00[AMR][1000 genomes]
rs73839116	1.00[AMR][1000 genomes]
rs73839117	1.00[AMR][1000 genomes]
rs7638914	1.00[AMR][1000 genomes]
rs7641255	1.00[AMR][1000 genomes];1.00[EUR][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	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv963321	chr3:52434961-52438226	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52395000-52443200	Weak transcription	Right Atrium	heart
2	chr3:52408000-52436600	Weak transcription	Fetal Kidney	kidney
3	chr3:52418600-52442200	Strong transcription	Fetal Intestine Small	intestine
4	chr3:52418800-52441800	Strong transcription	Brain Anterior Caudate	brain
5	chr3:52419000-52441800	Strong transcription	Liver	Liver
6	chr3:52419000-52442000	Strong transcription	Brain Hippocampus Middle	brain
7	chr3:52419000-52442600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:52419200-52441600	Strong transcription	Fetal Stomach	stomach
9	chr3:52419200-52441800	Strong transcription	Brain Angular Gyrus	brain
10	chr3:52419200-52442000	Strong transcription	Brain Inferior Temporal Lobe	brain
11	chr3:52420000-52442000	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:52420200-52442400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:52420200-52442400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:52420200-52442600	Strong transcription	Fetal Intestine Large	intestine
15	chr3:52422600-52441800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:52425600-52442000	Strong transcription	Spleen	Spleen
17	chr3:52426600-52442200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:52430000-52442400	Strong transcription	Brain Substantia Nigra	brain
19	chr3:52430200-52442000	Strong transcription	Primary T cells from cord blood	blood
20	chr3:52430800-52442600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr3:52430800-52442600	Strong transcription	Brain Cingulate Gyrus	brain
22	chr3:52431000-52441600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:52431200-52437200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr3:52431800-52437800	Strong transcription	Adipose Nuclei	Adipose
25	chr3:52431800-52440800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:52432000-52442400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:52432200-52440400	Strong transcription	Primary B cells from cord blood	blood
28	chr3:52432200-52442400	Strong transcription	Lung	lung
29	chr3:52432600-52439600	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr3:52432600-52442200	Strong transcription	Primary B cells from peripheral blood	blood
31	chr3:52432800-52436600	Weak transcription	NH-A	brain
32	chr3:52432800-52437200	Strong transcription	Fetal Muscle Leg	muscle
33	chr3:52432800-52437800	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:52432800-52437800	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:52432800-52441800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:52432800-52442000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:52432800-52442000	Strong transcription	Fetal Thymus	thymus
38	chr3:52432800-52442200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:52432800-52442400	Strong transcription	Thymus	Thymus
40	chr3:52432800-52442400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr3:52433000-52441600	Strong transcription	Fetal Brain Female	brain
42	chr3:52433000-52442400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:52433200-52442000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:52433200-52442000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:52433200-52442000	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:52433200-52442600	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr3:52433400-52436400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:52433400-52436600	Weak transcription	NHDF-Ad	bronchial
49	chr3:52433400-52439000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:52433400-52441200	Strong transcription	Primary T helper cells PMA-I stimulated	--

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