Variant report

Variant	rs3829697
Chromosome Location	chr20:1449495-1449496
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:1446816-1449625	HL-60	blood:	n/a	n/a
2	CHD2	chr20:1449433-1449927	K562	blood:	n/a	n/a
3	POLR2A	chr20:1446745-1449642	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr20:1405279..1407726-chr20:1449432..1451429,2	K562	blood:
2	chr20:1444656..1446589-chr20:1449305..1450879,2	K562	blood:
3	chr20:1449411..1451368-chr20:1451842..1453963,2	K562	blood:
4	chr20:1372232..1375944-chr20:1446656..1450761,3	MCF-7	breast:
5	chr20:1438711..1441119-chr20:1449312..1450919,2	MCF-7	breast:
6	chr20:1304611..1307577-chr20:1447050..1450049,5	K562	blood:
7	chr20:1443012..1448397-chr20:1448655..1450616,4	MCF-7	breast:
8	chr20:1408581..1410916-chr20:1448637..1451105,2	K562	blood:

No data

Variant related genes	Relation type
NSFL1C	TF binding region
ENSG00000125775	Chromatin interaction
ENSG00000234684	Chromatin interaction
ENSG00000088833	Chromatin interaction
ENSG00000088832	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12480584	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12481007	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12481707	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16994239	1.00[JPT][hapmap]
rs17793360	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884390	1.00[JPT][hapmap]
rs1884393	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064645	1.00[JPT][hapmap]
rs2064646	1.00[JPT][hapmap]
rs2273321	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2873522	1.00[JPT][hapmap]
rs41275406	1.00[ASN][1000 genomes]
rs6033935	1.00[JPT][hapmap]
rs6105101	1.00[JPT][hapmap]
rs6109984	1.00[JPT][hapmap]
rs6109989	1.00[JPT][hapmap]
rs8118710	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8123855	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs984497	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs984498	0.93[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer 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 lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv1850632	chr20:1393861-1465597	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv833893	chr20:1414615-1527779	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1447600-1449800	Weak transcription	Small Intestine	intestine
2	chr20:1447600-1450000	Weak transcription	Aorta	Aorta
3	chr20:1448000-1449600	Weak transcription	HSMM	muscle
4	chr20:1448000-1449600	Weak transcription	Osteobl	bone
5	chr20:1448000-1449800	Weak transcription	HSMMtube	muscle
6	chr20:1448000-1450200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr20:1448000-1450200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr20:1448000-1450200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr20:1448200-1449600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr20:1448200-1449600	Weak transcription	Liver	Liver
11	chr20:1448200-1449600	Weak transcription	HMEC	breast
12	chr20:1448200-1449600	Weak transcription	HUVEC	blood vessel
13	chr20:1448200-1449800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr20:1448200-1449800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr20:1448200-1450200	Weak transcription	Right Ventricle	heart
16	chr20:1448200-1450200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr20:1448200-1450200	Weak transcription	NHEK	skin
18	chr20:1448200-1450400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr20:1448200-1450400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr20:1448200-1450600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr20:1448200-1450800	Weak transcription	Right Atrium	heart
22	chr20:1448200-1451200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr20:1448200-1451600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr20:1448200-1451600	Enhancers	Placenta	Placenta
25	chr20:1448200-1451600	Enhancers	Stomach Mucosa	stomach
26	chr20:1448200-1452200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr20:1448200-1455800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr20:1448200-1457400	Weak transcription	Spleen	Spleen
29	chr20:1448200-1459000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr20:1448400-1449600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr20:1448400-1449600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr20:1448400-1449600	Bivalent Enhancer	Fetal Thymus	thymus
33	chr20:1448400-1449600	Weak transcription	A549	lung
34	chr20:1448400-1450000	Weak transcription	Hela-S3	cervix
35	chr20:1448400-1450200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr20:1448400-1450200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr20:1448400-1450600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr20:1448400-1450600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr20:1448400-1450600	Enhancers	Pancreas	Pancrea
40	chr20:1448400-1450800	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr20:1448400-1450800	Enhancers	Adipose Nuclei	Adipose
42	chr20:1448400-1452200	Weak transcription	Esophagus	oesophagus
43	chr20:1448600-1450200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr20:1448600-1450400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr20:1448600-1450400	Weak transcription	Fetal Muscle Leg	muscle
46	chr20:1448600-1451400	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr20:1448800-1449600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr20:1448800-1450800	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr20:1448800-1452000	Enhancers	Duodenum Mucosa	Duodenum
50	chr20:1448800-1452000	Enhancers	Rectal Mucosa Donor 29	rectum

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