Variant report

Variant	rs804996
Chromosome Location	chr3:120285772-120285773
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:120284576..120286509-chr3:120313591..120316096,2	K562	blood:
2	chr3:120285088..120287233-chr3:120289069..120290878,2	K562	blood:
3	chr3:120285518..120287941-chr3:120460010..120462833,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000065518	Chromatin interaction
ENSG00000144840	Chromatin interaction
ENSG00000153767	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1259482	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1259484	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1259486	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1259496	0.85[EUR][1000 genomes]
rs1272777	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1370741	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4676799	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs804995	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs804997	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804999	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs805000	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs805001	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs805003	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805005	0.88[ASN][1000 genomes]
rs805006	0.88[ASN][1000 genomes]
rs805007	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs805008	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs810867	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv508238	chr3:120248574-120329424	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	esv3373301	chr3:120273762-120421260	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
8	esv3404272	chr3:120274212-120294960	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120278800-120286200	Weak transcription	HSMMtube	muscle
2	chr3:120278800-120286800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:120279800-120286200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:120279800-120286200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:120279800-120287000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:120279800-120288000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:120280000-120285800	Weak transcription	Fetal Stomach	stomach
8	chr3:120280000-120286200	Weak transcription	Liver	Liver
9	chr3:120280000-120286800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:120280600-120285800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:120280600-120285800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:120280800-120286000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:120280800-120286000	Weak transcription	Osteobl	bone
14	chr3:120280800-120286200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:120280800-120286200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:120280800-120286200	Weak transcription	Hela-S3	cervix
17	chr3:120280800-120286400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:120282800-120286000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:120282800-120291000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:120284200-120286400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:120284600-120286200	Weak transcription	Fetal Heart	heart
22	chr3:120285000-120286400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:120285000-120287400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr3:120285000-120289200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr3:120285400-120285800	Enhancers	H1 Cell Line	embryonic stem cell
26	chr3:120285400-120285800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:120285400-120285800	Enhancers	H9 Cell Line	embryonic stem cell
28	chr3:120285400-120286200	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr3:120285400-120286200	Enhancers	Brain Cingulate Gyrus	brain
30	chr3:120285400-120286400	Enhancers	Brain Angular Gyrus	brain
31	chr3:120285400-120286400	Enhancers	Brain Anterior Caudate	brain
32	chr3:120285400-120286400	Enhancers	Colon Smooth Muscle	Colon
33	chr3:120285400-120286600	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr3:120285400-120287000	Enhancers	Brain Germinal Matrix	brain
35	chr3:120285400-120287000	Enhancers	Duodenum Mucosa	Duodenum
36	chr3:120285400-120287200	Enhancers	Rectal Smooth Muscle	rectum
37	chr3:120285400-120288600	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr3:120285400-120288600	Enhancers	Brain Hippocampus Middle	brain
39	chr3:120285400-120288600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:120285400-120288600	Enhancers	Brain Substantia Nigra	brain
41	chr3:120285400-120288800	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr3:120285600-120286200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr3:120285600-120286200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr3:120285600-120286200	Enhancers	Ovary	ovary
45	chr3:120285600-120286200	Enhancers	A549	lung
46	chr3:120285600-120286400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:120285600-120286400	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr3:120285600-120286400	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr3:120285600-120286800	Enhancers	Fetal Lung	lung
50	chr3:120285600-120287200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links