Variant report

Variant	rs16842157
Chromosome Location	chr1:223957151-223957152
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:223957114-223958466	U87	brain:	n/a	n/a
2	POLR2A	chr1:223956590-223957719	K562	blood:	n/a	n/a
3	POLR2A	chr1:223956518-223969626	K562	blood:	n/a	n/a
4	POLR2A	chr1:223956762-223960838	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223888744..223890349-chr1:223956680..223958231,2	MCF-7	breast:

Variant related genes	Relation type
CAPN2	TF binding region
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12038706	1.00[AMR][1000 genomes]
rs16842168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16842198	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370148	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370180	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370183	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56831338	1.00[AMR][1000 genomes]
rs57108544	1.00[AMR][1000 genomes]
rs57153784	1.00[AMR][1000 genomes]
rs58391315	1.00[AMR][1000 genomes]
rs59173114	1.00[AMR][1000 genomes]
rs60245976	1.00[AMR][1000 genomes]
rs60956486	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73114404	1.00[AMR][1000 genomes]
rs73114482	1.00[AMR][1000 genomes]
rs73114500	1.00[AMR][1000 genomes]
rs73115632	1.00[AMR][1000 genomes]
rs73116433	1.00[AMR][1000 genomes]
rs73116444	1.00[AMR][1000 genomes]
rs73116448	1.00[AMR][1000 genomes]
rs73127419	1.00[AMR][1000 genomes]
rs73127431	1.00[AMR][1000 genomes]
rs73127434	1.00[AMR][1000 genomes]
rs73127439	1.00[AMR][1000 genomes]
rs73128039	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73128040	1.00[AMR][1000 genomes]
rs73128044	1.00[AMR][1000 genomes]
rs73131132	1.00[AMR][1000 genomes]
rs73131150	1.00[AMR][1000 genomes]
rs73131157	1.00[AMR][1000 genomes]
rs73131162	1.00[AMR][1000 genomes]
rs73131164	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223937000-223957200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:223937000-223959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:223937000-223960000	Weak transcription	Thymus	Thymus
4	chr1:223937200-223958400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:223937200-223958400	Weak transcription	Fetal Heart	heart
6	chr1:223941000-223957600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:223941000-223958200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:223941000-223959400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:223941200-223961600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:223942400-223958800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:223947000-223957200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:223948000-223957600	Weak transcription	Fetal Brain Male	brain
13	chr1:223948400-223957200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:223949600-223958400	Weak transcription	Small Intestine	intestine
15	chr1:223950000-223957600	Weak transcription	Right Atrium	heart
16	chr1:223951400-223957200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr1:223952000-223957200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:223954000-223957200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:223954200-223957200	Weak transcription	Brain Angular Gyrus	brain
20	chr1:223954200-223957200	Weak transcription	Brain Germinal Matrix	brain
21	chr1:223954200-223957200	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:223954200-223957400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:223954200-223958800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:223954400-223957200	Weak transcription	Brain Substantia Nigra	brain
25	chr1:223954400-223957200	Weak transcription	Spleen	Spleen
26	chr1:223954400-223957200	Weak transcription	Hela-S3	cervix
27	chr1:223954400-223957200	Weak transcription	HSMMtube	muscle
28	chr1:223954400-223958600	Weak transcription	Ovary	ovary
29	chr1:223954400-223961800	Weak transcription	HepG2	liver
30	chr1:223954800-223957200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:223954800-223957200	Weak transcription	NHDF-Ad	bronchial
32	chr1:223954800-223964000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:223956400-223957400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:223956400-223958400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:223956600-223957200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:223956600-223957200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:223956600-223957200	Strong transcription	HSMM	muscle
38	chr1:223956600-223957200	Strong transcription	NHEK	skin
39	chr1:223956600-223957400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:223956600-223957400	Strong transcription	K562	blood
41	chr1:223956600-223957600	Strong transcription	Osteobl	bone
42	chr1:223956600-223957800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:223956600-223957800	ZNF genes & repeats	Fetal Thymus	thymus
44	chr1:223956600-223957800	Strong transcription	A549	lung
45	chr1:223956600-223958000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:223956600-223958000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:223956600-223958000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:223956600-223958000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:223956600-223958000	Strong transcription	NH-A	brain
50	chr1:223956600-223958200	Strong transcription	Fetal Intestine Small	intestine

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