Variant report

Variant	rs1653599
Chromosome Location	chr12:121664865-121664866
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:121660603..121665110-chr12:121671733..121676729,4	K562	blood:
2	chr12:121664342..121666780-chr12:121734216..121737104,3	MCF-7	breast:
3	chr12:121604725..121607272-chr12:121663466..121665293,2	MCF-7	breast:
4	chr12:121654852..121658533-chr12:121664523..121668061,3	K562	blood:
5	chr12:121659173..121660678-chr12:121664466..121666483,2	K562	blood:
6	chr12:121661400..121663391-chr12:121663416..121665222,3	MCF-7	breast:
7	chr12:121659123..121660673-chr12:121663523..121665966,2	K562	blood:
8	chr12:121660136..121663309-chr12:121663557..121666409,5	MCF-7	breast:
9	chr12:121646468..121649464-chr12:121663700..121666381,2	K562	blood:
10	chr12:121646834..121652613-chr12:121661734..121667006,9	MCF-7	breast:
11	chr12:121664133..121666878-chr12:121668504..121670264,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000110931	Chromatin interaction
ENSG00000135124	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1169716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1169719	1.00[AMR][1000 genomes]
rs1169723	1.00[AMR][1000 genomes]
rs1169724	1.00[AMR][1000 genomes]
rs1169810	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1180013	1.00[AMR][1000 genomes]
rs1180014	1.00[AMR][1000 genomes]
rs1180016	1.00[AMR][1000 genomes]
rs1186053	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1630178	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1647255	1.00[AMR][1000 genomes]
rs1653587	0.82[AFR][1000 genomes]
rs1653588	0.82[AFR][1000 genomes]
rs1653589	0.82[AFR][1000 genomes]
rs1653600	1.00[AMR][1000 genomes]
rs1653615	1.00[AMR][1000 genomes]
rs1718110	1.00[AMR][1000 genomes]
rs1718156	0.82[AFR][1000 genomes]
rs1718157	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1794891	1.00[AMR][1000 genomes]
rs1794903	1.00[AMR][1000 genomes]
rs1796418	1.00[AMR][1000 genomes]
rs1975123	1.00[AMR][1000 genomes]
rs208281	1.00[AMR][1000 genomes]
rs208285	1.00[AMR][1000 genomes]
rs208286	1.00[AMR][1000 genomes]
rs208297	1.00[AMR][1000 genomes]
rs2116500	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2116501	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2252298	0.82[AFR][1000 genomes]
rs2252304	0.82[AFR][1000 genomes]
rs2393848	1.00[AMR][1000 genomes]
rs2567982	0.82[AFR][1000 genomes]
rs2567983	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2567998	1.00[AMR][1000 genomes]
rs2568004	1.00[AMR][1000 genomes]
rs2668248	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2686365	1.00[AMR][1000 genomes]
rs2686366	1.00[AMR][1000 genomes]
rs2686381	1.00[AMR][1000 genomes]
rs2686383	1.00[AMR][1000 genomes]
rs2708094	1.00[AMR][1000 genomes]
rs2948125	1.00[AMR][1000 genomes]
rs3861796	1.00[AMR][1000 genomes]
rs512239	1.00[AMR][1000 genomes]
rs566496	1.00[AMR][1000 genomes]
rs584133	1.00[AMR][1000 genomes]
rs657647	1.00[AMR][1000 genomes]
rs672632	1.00[AMR][1000 genomes]
rs680700	1.00[AMR][1000 genomes]
rs682104	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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv899564	chr12:121641509-121689798	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv899565	chr12:121641509-121698785	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121648800-121666600	Weak transcription	Ovary	ovary
2	chr12:121649000-121665000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:121649000-121666600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:121649000-121675800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr12:121649000-121676200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:121649000-121676200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr12:121649000-121676600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr12:121649400-121680200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:121652400-121675600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:121653200-121665000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:121653200-121666400	Weak transcription	Colon Smooth Muscle	Colon
12	chr12:121653200-121675600	Weak transcription	HSMMtube	muscle
13	chr12:121653200-121698800	Weak transcription	Fetal Heart	heart
14	chr12:121653400-121665000	Weak transcription	NHEK	skin
15	chr12:121653400-121673600	Weak transcription	Osteobl	bone
16	chr12:121653400-121677600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:121653400-121678600	Weak transcription	Right Atrium	heart
18	chr12:121653600-121670200	Weak transcription	NHDF-Ad	bronchial
19	chr12:121654800-121675200	Strong transcription	Fetal Stomach	stomach
20	chr12:121655200-121678000	Weak transcription	Fetal Kidney	kidney
21	chr12:121655400-121667400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr12:121655400-121667800	Weak transcription	A549	lung
23	chr12:121656000-121666600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:121656600-121666600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:121657000-121671600	Weak transcription	HUVEC	blood vessel
26	chr12:121657000-121676200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr12:121657200-121665000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:121657200-121666400	Weak transcription	Brain Substantia Nigra	brain
29	chr12:121658200-121673600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:121658800-121671600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr12:121659400-121667600	Strong transcription	Fetal Muscle Leg	muscle
32	chr12:121659600-121665200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr12:121660400-121665600	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr12:121660600-121665400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:121660600-121665600	Enhancers	Primary T cells from cord blood	blood
36	chr12:121660600-121665600	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr12:121660600-121665600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:121660600-121666000	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr12:121660800-121665600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr12:121660800-121667600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr12:121661000-121666600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr12:121661600-121666600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:121661600-121666600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:121661600-121667600	Weak transcription	Hela-S3	cervix
45	chr12:121661600-121667800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr12:121661600-121675800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr12:121661600-121675800	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr12:121661800-121665000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr12:121661800-121665800	Enhancers	Primary T cells fromperipheralblood	blood
50	chr12:121661800-121665800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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