Variant report

Variant	rs16828378
Chromosome Location	chr2:151466594-151466595
allele	A/C
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	TCF12	chr2:151466243-151466921	A549	lung:	n/a	n/a
2	MAFK	chr2:151466401-151466767	IMR90	lung:	n/a	chr2:151466556-151466565
3	MAX	chr2:151466325-151466728	SK-N-SH	brain:	n/a	n/a
4	RAD21	chr2:151466361-151467686	IMR90	lung:	n/a	chr2:151467389-151467408
5	PBX3	chr2:151466317-151466846	SK-N-SH	brain:	n/a	n/a
6	FOXP2	chr2:151466374-151466698	SK-N-MC	brain:	n/a	n/a
7	FOXP2	chr2:151466391-151466653	SK-N-MC	brain:	n/a	n/a
8	EP300	chr2:151466120-151466998	SK-N-SH	brain:	n/a	n/a
9	JUND	chr2:151466280-151466920	SK-N-SH	brain:	n/a	n/a
10	TEAD4	chr2:151466264-151466958	SK-N-SH	brain:	n/a	n/a
11	GATA3	chr2:151466159-151467016	SK-N-SH	brain:	n/a	n/a
12	FOSL2	chr2:151466243-151466765	SK-N-SH	brain:	n/a	n/a
13	TCF12	chr2:151466111-151467677	SK-N-SH	brain:	n/a	n/a
14	PBX3	chr2:151466160-151466962	SK-N-SH	brain:	n/a	n/a
15	CTCF	chr2:151466342-151467958	A549	lung:	n/a	chr2:151467393-151467406 chr2:151467391-151467409 chr2:151467392-151467408
16	MXI1	chr2:151466194-151467708	IMR90	lung:	n/a	n/a
17	POLR2A	chr2:151466319-151466722	SK-N-MC	brain:	n/a	n/a
18	STAT3	chr2:151466570-151466635	MCF10A-Er-Src	breast:	n/a	n/a
19	TCF12	chr2:151466194-151466986	SK-N-SH	brain:	n/a	n/a
20	EP300	chr2:151466129-151466987	SK-N-SH	brain:	n/a	n/a
21	EP300	chr2:151466417-151466831	A549	lung:	n/a	n/a
22	TEAD4	chr2:151466163-151466995	SK-N-SH	brain:	n/a	n/a
23	GATA3	chr2:151466223-151466941	SK-N-SH	brain:	n/a	n/a
24	MAX	chr2:151466237-151466751	SK-N-SH	brain:	n/a	n/a
25	EP300	chr2:151466318-151466698	SK-N-SH_RA	brain:	n/a	n/a
26	NFIC	chr2:151466186-151466985	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr2:151466296-151466796	SK-N-SH	brain:	n/a	n/a
28	SMC3	chr2:151466185-151467763	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:151338744..151345527-chr2:151464975..151472294,14	MCF-7	breast:
2	chr2:150453295..150455757-chr2:151465590..151467443,2	MCF-7	breast:
3	chr2:151466148..151468883-chr2:151471106..151473302,2	MCF-7	breast:
4	chr2:151340761..151344289-chr2:151463016..151468103,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224048	TF binding region
ENSG00000115963	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs16828340	0.91[AMR][1000 genomes]
rs6740555	0.85[AFR][1000 genomes];0.81[AMR][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	nsv1001838	chr2:150819672-151745876	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv535980	chr2:150819672-151745876	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv532473	chr2:151164210-151701860	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv834415	chr2:151374254-151558649	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv2757836	chr2:151457277-151844210	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	esv2759096	chr2:151457277-151844210	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16828378	RIF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:151458200-151469400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:151458600-151467000	Weak transcription	NHEK	skin
3	chr2:151458600-151469400	Weak transcription	Aorta	Aorta
4	chr2:151462800-151466600	Enhancers	NHDF-Ad	bronchial
5	chr2:151462800-151471000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:151463000-151467400	Enhancers	HSMMtube	muscle
7	chr2:151463000-151467600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:151463000-151467600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:151463400-151467600	Enhancers	NHLF	lung
10	chr2:151464200-151467000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:151464200-151467000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:151464400-151476200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:151465200-151467200	Weak transcription	HMEC	breast
14	chr2:151465400-151466800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:151465600-151467400	Enhancers	A549	lung
16	chr2:151466000-151467400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr2:151466200-151466600	Flanking Active TSS	Osteobl	bone
18	chr2:151466200-151466800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:151466200-151466800	Enhancers	Rectal Smooth Muscle	rectum
20	chr2:151466200-151467000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:151466200-151467200	Enhancers	HSMM	muscle
22	chr2:151466200-151467400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:151466200-151467400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:151466200-151467400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr2:151466200-151469600	Weak transcription	Fetal Muscle Leg	muscle
26	chr2:151466400-151467000	Enhancers	Colon Smooth Muscle	Colon
27	chr2:151466400-151467000	Enhancers	Fetal Lung	lung
28	chr2:151466400-151467400	Enhancers	Adipose Nuclei	Adipose
29	chr2:151466400-151467400	Enhancers	Liver	Liver
30	chr2:151466400-151467400	Enhancers	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links