Variant report

Variant	rs3860349
Chromosome Location	chr1:95287080-95287081
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:95285521-95287704	HepG2	liver:	n/a	n/a
2	ARID3A	chr1:95286999-95287507	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:95285937..95287907-chr1:95288541..95290164,2	MCF-7	breast:

Variant related genes	Relation type
LINC01057	TF binding region
SLC44A3	TF binding region
ENSG00000143036	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10782992	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10782993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10874894	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1146458	1.00[ASN][1000 genomes]
rs2893277	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3860339	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3860345	1.00[ASN][1000 genomes]
rs3860348	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3904553	1.00[ASN][1000 genomes]
rs3904554	1.00[ASN][1000 genomes]
rs3916208	1.00[ASN][1000 genomes]
rs3916432	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3936924	0.83[AMR][1000 genomes]
rs4847359	0.82[ASW][hapmap];1.00[CHD][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6541370	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6541372	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6665321	1.00[ASN][1000 genomes]
rs6702030	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7528707	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7543977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9432373	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001587	chr1:95027691-95318680	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95283800-95287600	Active TSS	Fetal Intestine Large	intestine
2	chr1:95284200-95288000	Active TSS	Fetal Intestine Small	intestine
3	chr1:95284800-95287200	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr1:95284800-95287600	Active TSS	Pancreas	Pancrea
5	chr1:95284800-95287800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr1:95285600-95287200	Active TSS	Rectal Mucosa Donor 31	rectum
7	chr1:95285600-95287800	Active TSS	Duodenum Mucosa	Duodenum
8	chr1:95285600-95287800	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr1:95285800-95287400	Enhancers	Fetal Heart	heart
10	chr1:95285800-95287800	Active TSS	Colonic Mucosa	Colon
11	chr1:95285800-95287800	Active TSS	Rectal Smooth Muscle	rectum
12	chr1:95286400-95287200	Flanking Active TSS	Liver	Liver
13	chr1:95286400-95288000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:95286400-95288200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:95286400-95288400	Enhancers	Fetal Muscle Leg	muscle
16	chr1:95286400-95293400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:95286400-95295800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:95286400-95295800	Weak transcription	Right Ventricle	heart
19	chr1:95286400-95298800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:95286600-95287200	Bivalent Enhancer	Fetal Brain Male	brain
21	chr1:95286600-95287400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:95286600-95287400	Active TSS	Stomach Mucosa	stomach
23	chr1:95286600-95287800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:95286600-95287800	Active TSS	Fetal Stomach	stomach
25	chr1:95286600-95289000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:95286600-95292400	Weak transcription	Right Atrium	heart
27	chr1:95286600-95296400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:95286600-95311800	Weak transcription	Placenta	Placenta
29	chr1:95286600-95319800	Weak transcription	Lung	lung
30	chr1:95286800-95287200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
31	chr1:95286800-95287200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:95286800-95287200	Flanking Active TSS	Fetal Kidney	kidney
33	chr1:95286800-95287400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
34	chr1:95286800-95287600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:95286800-95287600	Weak transcription	Gastric	stomach
36	chr1:95286800-95287800	Weak transcription	Fetal Brain Female	brain
37	chr1:95286800-95287800	Enhancers	Placenta Amnion	Placenta Amnion
38	chr1:95286800-95288400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:95286800-95290600	Weak transcription	Esophagus	oesophagus
40	chr1:95287000-95287200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:95287000-95287200	Flanking Active TSS	HSMMtube	muscle
42	chr1:95287000-95287400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
43	chr1:95287000-95287400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:95287000-95287600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
45	chr1:95287000-95287600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr1:95287000-95287800	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr1:95287000-95287800	Enhancers	A549	lung
48	chr1:95287000-95287800	Flanking Active TSS	HepG2	liver
49	chr1:95287000-95288000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
50	chr1:95287000-95289000	Enhancers	Fetal Lung	lung

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