Variant report

Variant	rs10153924
Chromosome Location	chr2:99385059-99385060
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99344922..99348721-chr2:99382903..99389092,6	MCF-7	breast:
2	chr2:99345368..99349321-chr2:99385005..99390572,6	MCF-7	breast:
3	chr2:99384896..99387607-chr2:99394803..99397192,2	MCF-7	breast:
4	chr2:99342701..99345080-chr2:99384089..99385650,2	MCF-7	breast:
5	chr2:99224143..99225880-chr2:99384607..99386778,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C2orf55-1	chr2:99384249-99385249	XLOC_002221

Variant related genes	Relation type
ENSG00000183513	Chromatin interaction
ENSG00000071073	Chromatin interaction
ENSG00000115446	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11123753	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12232948	0.92[EUR][1000 genomes]
rs12233010	1.00[AFR][1000 genomes]
rs12233187	1.00[AFR][1000 genomes]
rs12233197	1.00[AFR][1000 genomes]
rs1399512	1.00[ASN][1000 genomes]
rs1517679	1.00[ASN][1000 genomes]
rs1517680	1.00[ASN][1000 genomes]
rs1574516	1.00[AFR][1000 genomes]
rs4850884	1.00[ASN][1000 genomes]
rs4850886	1.00[ASN][1000 genomes]
rs4850887	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851149	1.00[ASN][1000 genomes]
rs4851152	1.00[ASN][1000 genomes]
rs4851155	1.00[ASN][1000 genomes]
rs4851156	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851157	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851158	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851159	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67008211	1.00[ASN][1000 genomes]
rs72811067	1.00[ASN][1000 genomes]
rs72811068	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72811073	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72811074	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72811075	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72811079	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72811084	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72811092	0.83[AMR][1000 genomes]
rs72811098	0.88[AMR][1000 genomes]
rs72811102	0.88[AMR][1000 genomes]
rs72813003	0.88[AMR][1000 genomes]
rs72813009	1.00[AFR][1000 genomes]
rs72813012	1.00[AFR][1000 genomes]
rs72813013	1.00[AFR][1000 genomes]
rs72813021	1.00[AFR][1000 genomes]
rs72821966	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99373800-99388000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:99375200-99386200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:99375200-99386400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:99377000-99386400	Weak transcription	Esophagus	oesophagus
5	chr2:99378400-99389400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:99378800-99388200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:99379200-99388200	Weak transcription	Brain Substantia Nigra	brain
8	chr2:99379400-99385200	Weak transcription	Fetal Brain Male	brain
9	chr2:99379400-99385200	Weak transcription	Right Atrium	heart
10	chr2:99379400-99386400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:99379400-99388400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:99380600-99387400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:99380600-99387400	Weak transcription	Adipose Nuclei	Adipose
14	chr2:99381000-99386200	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr2:99382000-99386200	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr2:99382000-99386800	Enhancers	GM12878-XiMat	blood
17	chr2:99382200-99385400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:99382200-99385400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr2:99382200-99385600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:99382200-99386400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:99382200-99386400	Enhancers	Duodenum Mucosa	Duodenum
22	chr2:99382400-99385400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr2:99382400-99386200	Enhancers	Primary T cells fromperipheralblood	blood
24	chr2:99382400-99386200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:99382600-99385200	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr2:99382600-99385400	Enhancers	Primary T cells from cord blood	blood
27	chr2:99382600-99386200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr2:99383600-99385200	Weak transcription	Stomach Mucosa	stomach
29	chr2:99383600-99385400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:99383600-99385400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr2:99383800-99385600	Enhancers	Small Intestine	intestine
32	chr2:99383800-99387000	Enhancers	HUVEC	blood vessel
33	chr2:99384200-99386600	Weak transcription	Fetal Intestine Small	intestine
34	chr2:99384400-99389800	Flanking Active TSS	Dnd41	blood
35	chr2:99384600-99386200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:99384800-99385400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:99384800-99385400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:99384800-99385600	Enhancers	NH-A	brain
39	chr2:99384800-99385800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr2:99384800-99385800	Enhancers	Muscle Satellite Cultured Cells	--
41	chr2:99384800-99385800	Enhancers	HMEC	breast
42	chr2:99384800-99386000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:99384800-99386800	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr2:99384800-99388400	Enhancers	Placenta	Placenta
45	chr2:99385000-99385200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:99385000-99385200	Flanking Active TSS	Brain Hippocampus Middle	brain
47	chr2:99385000-99385400	Enhancers	Fetal Kidney	kidney
48	chr2:99385000-99385400	Flanking Active TSS	Fetal Thymus	thymus
49	chr2:99385000-99385400	Enhancers	Osteobl	bone
50	chr2:99385000-99385600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin

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