Variant report

Variant	rs3769720
Chromosome Location	chr2:99124345-99124346
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:99124298..99126771-chr2:99127183..99129014,2	K562	blood:
2	chr2:99124310..99124811-chr2:128568506..128569006,2	NB4	blood:
3	chr2:99124187..99127172-chr2:99129019..99132025,3	K562	blood:
4	chr2:99104757..99106560-chr2:99122762..99124646,2	K562	blood:
5	chr2:99079622..99082074-chr2:99124173..99125944,2	K562	blood:
6	chr2:99114971..99120077-chr2:99122258..99125912,6	K562	blood:
7	chr2:99121740..99124378-chr2:99222432..99225473,3	K562	blood:
8	chr2:99118086..99120077-chr2:99123851..99125912,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000115446	Chromatin interaction
ENSG00000183513	Chromatin interaction
ENSG00000136709	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs13395005	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13429817	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17030716	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17502330	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2271041	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3171842	1.00[ASN][1000 genomes]
rs3731655	1.00[ASN][1000 genomes]
rs3769704	0.87[ASN][1000 genomes]
rs3769722	1.00[ASN][1000 genomes]
rs3769731	1.00[ASN][1000 genomes]
rs3769732	1.00[ASN][1000 genomes]
rs3769742	1.00[ASN][1000 genomes]
rs3820944	1.00[ASN][1000 genomes]
rs41460047	1.00[ASN][1000 genomes]
rs7564438	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7589617	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7602422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7604711	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9631039	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1006328	chr2:98977192-99210376	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1007244	chr2:99063753-99136472	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1013941	chr2:99116255-99317933	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv535834	chr2:99116255-99317933	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv2840	chr2:99116934-99162190	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99101600-99131400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:99112200-99130600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:99114000-99137600	Weak transcription	Fetal Intestine Large	intestine
4	chr2:99114400-99131200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr2:99114400-99154000	Weak transcription	HepG2	liver
6	chr2:99115000-99135000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:99116600-99137800	Weak transcription	Fetal Brain Female	brain
8	chr2:99116800-99135600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr2:99117200-99131200	Weak transcription	Fetal Kidney	kidney
10	chr2:99118000-99124800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr2:99118000-99126000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:99118000-99129400	Genic enhancers	Primary T cells from cord blood	blood
13	chr2:99118200-99125000	Enhancers	Spleen	Spleen
14	chr2:99118200-99126000	Enhancers	Brain Anterior Caudate	brain
15	chr2:99118200-99126200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr2:99118600-99124600	Weak transcription	Stomach Mucosa	stomach
17	chr2:99118600-99125200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:99118600-99125800	Enhancers	Colon Smooth Muscle	Colon
19	chr2:99119000-99126000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:99119200-99124400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:99119200-99126400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr2:99119200-99137400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:99119400-99130600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:99119400-99131400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:99119600-99124400	Weak transcription	NH-A	brain
26	chr2:99119600-99124800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr2:99119600-99131400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:99120200-99126800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr2:99120600-99131200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:99120600-99131400	Weak transcription	Dnd41	blood
31	chr2:99120800-99124600	Enhancers	Primary B cells from cord blood	blood
32	chr2:99121000-99124800	Enhancers	Duodenum Mucosa	Duodenum
33	chr2:99121400-99131200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:99121400-99135800	Weak transcription	Aorta	Aorta
35	chr2:99121600-99124800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:99121600-99125400	Enhancers	Fetal Muscle Trunk	muscle
37	chr2:99121600-99155400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:99121800-99125800	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr2:99121800-99136400	Weak transcription	Gastric	stomach
40	chr2:99122000-99124800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr2:99122000-99125200	Enhancers	Primary B cells from peripheral blood	blood
42	chr2:99122000-99130800	Weak transcription	Ovary	ovary
43	chr2:99122000-99131400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:99122200-99126000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr2:99122200-99135800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:99122600-99125000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:99122600-99125000	Enhancers	Fetal Muscle Leg	muscle
48	chr2:99122600-99125600	Enhancers	Left Ventricle	heart
49	chr2:99122600-99125800	Enhancers	Brain Substantia Nigra	brain
50	chr2:99122600-99125800	Enhancers	Placenta	Placenta

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