Variant report

Variant	rs2236399
Chromosome Location	chr1:120286457-120286458
allele	G/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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:120278740..120281495-chr1:120284812..120287109,2	MCF-7	breast:
2	chr1:120278483..120280232-chr1:120286168..120288570,2	K562	blood:
3	chr1:120240386..120241937-chr1:120285386..120286899,2	MCF-7	breast:
4	chr1:120286454..120287367-chr1:120413250..120414231,6	MCF-7	breast:
5	chr1:120286431..120287491-chr1:120351403..120352218,5	MCF-7	breast:
6	chr1:120286305..120287642-chr1:120412794..120414270,15	MCF-7	breast:
7	chr1:120286100..120288877-chr1:120290549..120293981,3	K562	blood:
8	chr1:120286457..120287055-chr1:120510730..120511435,2	MCF-7	breast:
9	chr1:120278363..120280873-chr1:120284153..120287954,3	K562	blood:
10	chr1:120286445..120287336-chr1:120428589..120429153,3	MCF-7	breast:
11	chr1:120281250..120283814-chr1:120284593..120287866,3	K562	blood:
12	chr1:120286420..120287121-chr1:232656270..232657169,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000092621	Chromatin interaction
ENSG00000226446	Chromatin interaction
ENSG00000134193	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10923897	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11487674	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070041	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12079115	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12406668	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2236400	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241868	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9943291	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer 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 target site	38 gene(s)	inside rSNPs	diseases
5	nsv831204	chr1:120266449-120314091	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS 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	20 gene(s)	inside rSNPs	diseases
8	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120257200-120287000	Weak transcription	NH-A	brain
2	chr1:120258600-120289200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:120260400-120287600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:120261000-120287200	Strong transcription	Hela-S3	cervix
5	chr1:120261600-120288200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:120261800-120287000	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:120261800-120287600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:120262000-120287200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:120262000-120287400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:120262000-120287400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:120262000-120287800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:120262000-120288200	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr1:120262400-120287400	Strong transcription	Dnd41	blood
14	chr1:120262400-120288200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:120263400-120286800	Strong transcription	Primary T cells from cord blood	blood
16	chr1:120263400-120287400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:120263400-120291400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:120267200-120286800	Weak transcription	Primary B cells from cord blood	blood
19	chr1:120269800-120286800	Weak transcription	Small Intestine	intestine
20	chr1:120271000-120286600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:120275200-120286800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:120278600-120287000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:120279200-120286600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr1:120279200-120290600	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr1:120280200-120286600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:120280400-120289400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:120280600-120286800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:120280800-120287000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:120281200-120287000	Weak transcription	K562	blood
30	chr1:120281600-120286600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:120281600-120286600	Strong transcription	Primary hematopoietic stem cells	blood
32	chr1:120282000-120293400	Weak transcription	Aorta	Aorta
33	chr1:120282200-120286600	Genic enhancers	Liver	Liver
34	chr1:120282400-120287400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:120282800-120287600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr1:120283200-120286600	Strong transcription	Fetal Thymus	thymus
37	chr1:120283200-120286800	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr1:120283600-120286600	Weak transcription	Fetal Kidney	kidney
39	chr1:120283600-120288600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:120283800-120286600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:120283800-120286800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:120283800-120286800	Enhancers	Right Ventricle	heart
43	chr1:120283800-120287200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:120284000-120288000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:120284200-120287400	Enhancers	Colon Smooth Muscle	Colon
46	chr1:120284400-120287200	Genic enhancers	Fetal Muscle Leg	muscle
47	chr1:120284400-120287800	Genic enhancers	Fetal Muscle Trunk	muscle
48	chr1:120284600-120286600	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr1:120284600-120286800	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr1:120284600-120286800	Weak transcription	Spleen	Spleen

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