Variant report

Variant	rs2501856
Chromosome Location	chr1:212856985-212856986
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212856876..212859074-chr1:212871826..212873912,2	K562	blood:
2	chr1:212856855..212858947-chr1:212862526..212864877,2	MCF-7	breast:
3	chr1:212780750..212783625-chr1:212854887..212857675,2	K562	blood:
4	chr1:212856703..212859262-chr1:212873284..212875727,3	K562	blood:
5	chr1:212851040..212855618-chr1:212856353..212859707,5	MCF-7	breast:
6	chr1:212855556..212859090-chr1:212860811..212864685,4	K562	blood:

Variant related genes	Relation type
ENSG00000123685	Chromatin interaction
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2456830	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2492780	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492788	0.95[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2501848	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2501849	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs906366	0.85[ASN][1000 genomes]
rs906367	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
5	esv1829918	chr1:212828460-212874731	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2501856	SNFT	cis	multi-tissue	Pritchard

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212853800-212860000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:212855400-212857600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr1:212855400-212857800	Flanking Active TSS	GM12878-XiMat	blood
4	chr1:212855600-212857600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr1:212855800-212857600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:212855800-212857800	Enhancers	Primary B cells from peripheral blood	blood
7	chr1:212855800-212857800	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr1:212855800-212857800	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:212855800-212858400	Enhancers	Primary B cells from cord blood	blood
10	chr1:212856000-212857000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:212856000-212857000	Enhancers	K562	blood
12	chr1:212856000-212857200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:212856000-212857600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr1:212856000-212857600	Enhancers	Adipose Nuclei	Adipose
15	chr1:212856000-212857600	Enhancers	Duodenum Mucosa	Duodenum
16	chr1:212856000-212858000	Enhancers	Primary T cells fromperipheralblood	blood
17	chr1:212856000-212858000	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr1:212856000-212858200	Enhancers	Spleen	Spleen
19	chr1:212856000-212867200	Weak transcription	Brain Anterior Caudate	brain
20	chr1:212856200-212857000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:212856200-212857400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:212856200-212857600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:212856200-212857600	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr1:212856200-212857800	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr1:212856200-212857800	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr1:212856200-212858000	Enhancers	Placenta	Placenta
27	chr1:212856200-212862600	Weak transcription	Lung	lung
28	chr1:212856400-212857200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
29	chr1:212856400-212857200	Enhancers	Dnd41	blood
30	chr1:212856600-212857000	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr1:212856600-212857200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:212856600-212857400	Enhancers	Primary T cells from cord blood	blood
33	chr1:212856600-212858200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr1:212856600-212861600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:212856800-212857000	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr1:212856800-212857000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:212856800-212857000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:212856800-212857000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:212856800-212857000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
40	chr1:212856800-212857200	Enhancers	H9 Cell Line	embryonic stem cell
41	chr1:212856800-212857200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:212856800-212857200	Enhancers	Fetal Thymus	thymus
43	chr1:212856800-212857400	Bivalent Enhancer	Colonic Mucosa	Colon
44	chr1:212856800-212857800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin

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