Variant report

Variant	rs62041348
Chromosome Location	chr16:79805937-79805938
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	BHLHE40	chr16:79805738-79806219	K562	blood:	n/a	n/a
2	RFX5	chr16:79803164-79806271	SK-N-SH	brain:	n/a	chr16:79804613-79804622 chr16:79804610-79804625 chr16:79804611-79804625

Variant related genes	Relation type
ENSG00000261390	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12443838	1.00[ASN][1000 genomes]
rs4313818	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4506911	0.92[ASN][1000 genomes]
rs56006814	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs56052219	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041304	0.83[AFR][1000 genomes]
rs62041307	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62041308	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041309	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041310	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041311	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs62041312	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041313	0.85[EUR][1000 genomes]
rs62041316	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs62041317	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs62041318	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs62041319	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs62041320	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs62041323	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62041324	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041325	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041326	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62041327	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041339	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041344	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62041345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62041346	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62041347	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62041349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62043341	0.83[AFR][1000 genomes]
rs62043342	0.83[AFR][1000 genomes]
rs62043343	0.83[AFR][1000 genomes]
rs62043344	1.00[AFR][1000 genomes]
rs62043358	0.83[AFR][1000 genomes]
rs7187139	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8053535	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv530714	chr16:79661581-79925435	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv833296	chr16:79692236-79889727	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv833297	chr16:79732501-79920419	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv2755409	chr16:79776699-79816299	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79805000-79806000	Enhancers	Fetal Thymus	thymus
2	chr16:79805000-79806200	Enhancers	Fetal Stomach	stomach
3	chr16:79805000-79806400	Enhancers	Fetal Lung	lung
4	chr16:79805000-79806600	Enhancers	Fetal Muscle Leg	muscle
5	chr16:79805000-79807400	Enhancers	Fetal Intestine Small	intestine
6	chr16:79805000-79807800	Enhancers	Fetal Intestine Large	intestine
7	chr16:79805000-79808800	Weak transcription	Esophagus	oesophagus
8	chr16:79805000-79809200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr16:79805000-79809400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr16:79805000-79810400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr16:79805200-79806000	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr16:79805200-79806200	Enhancers	Fetal Heart	heart
13	chr16:79805200-79806800	Enhancers	Colon Smooth Muscle	Colon
14	chr16:79805200-79806800	Enhancers	Duodenum Mucosa	Duodenum
15	chr16:79805200-79807000	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr16:79805200-79807000	Enhancers	Small Intestine	intestine
17	chr16:79805200-79808600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr16:79805200-79809000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr16:79805200-79809000	Weak transcription	NHEK	skin
20	chr16:79805200-79809200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr16:79805200-79809200	Weak transcription	HMEC	breast
22	chr16:79805200-79810000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr16:79805200-79810200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr16:79805200-79810200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr16:79805200-79810200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr16:79805200-79810200	Weak transcription	Brain Hippocampus Middle	brain
27	chr16:79805200-79810200	Weak transcription	NH-A	brain
28	chr16:79805400-79809400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr16:79805400-79810200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr16:79805400-79810200	Weak transcription	Adipose Nuclei	Adipose
31	chr16:79805400-79810200	Weak transcription	Thymus	Thymus
32	chr16:79805400-79810400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr16:79805400-79810400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr16:79805600-79806200	Enhancers	K562	blood
35	chr16:79805600-79810400	Weak transcription	Colonic Mucosa	Colon
36	chr16:79805800-79806200	Enhancers	Fetal Kidney	kidney
37	chr16:79805800-79806600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr16:79805800-79807200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links