Variant report

Variant	rs16844248
Chromosome Location	chr4:3387060-3387061
allele	C/G/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	chr4:3386687-3387513	HepG2	liver:	n/a	n/a
2	STAT3	chr4:3387046-3387272	MCF10A-Er-Src	breast:	n/a	n/a
3	HNF4A	chr4:3386621-3387060	HepG2	liver:	n/a	chr4:3386839-3386854 chr4:3386840-3386848 chr4:3386839-3386854
4	POLR2A	chr4:3386565-3387363	HepG2	liver:	n/a	n/a
5	POLR2A	chr4:3386948-3387516	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr4:3386875-3388105	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr4:3386733-3387339	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr4:3386537-3387069	HepG2	liver:	n/a	n/a
9	POLR2A	chr4:3386993-3387468	HUVEC	blood vessel:	n/a	n/a
10	HNF4G	chr4:3386577-3387090	HepG2	liver:	n/a	chr4:3386840-3386848 chr4:3386584-3386600 chr4:3386839-3386854
11	HNF4A	chr4:3386569-3387078	HepG2	liver:	n/a	chr4:3386839-3386854 chr4:3386840-3386848 chr4:3386584-3386600 chr4:3386839-3386854
12	STAT3	chr4:3387046-3387279	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr4:3387044-3387706	MCF10A-Er-Src	breast:	n/a	n/a
14	ELF1	chr4:3386996-3387550	GM12878	blood:	n/a	n/a
15	STAT3	chr4:3386932-3387271	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr4:3386902-3387593	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3386285..3389665-chr4:3485168..3487566,3	MCF-7	breast:

Variant related genes	Relation type
RGS12	TF binding region
ENSG00000175920	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11942127	1.00[AMR][1000 genomes]
rs11943410	1.00[AMR][1000 genomes]
rs16843151	1.00[AMR][1000 genomes]
rs16844266	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16844282	0.82[ASN][1000 genomes]
rs16844336	1.00[AMR][1000 genomes]
rs60881721	0.91[ASN][1000 genomes]
rs73795536	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv878463	chr4:3363994-3498896	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv428435	chr4:3386773-3623321	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3373000-3389000	Weak transcription	Psoas Muscle	Psoas
2	chr4:3373400-3388400	Weak transcription	Fetal Kidney	kidney
3	chr4:3373400-3388800	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:3375000-3389200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:3375400-3389600	Weak transcription	NHLF	lung
6	chr4:3378200-3388800	Weak transcription	Fetal Heart	heart
7	chr4:3378400-3388800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:3378400-3389000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr4:3378400-3389200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:3378400-3389200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:3378400-3390400	Weak transcription	Ovary	ovary
12	chr4:3378600-3389600	Weak transcription	Aorta	Aorta
13	chr4:3381000-3389000	Weak transcription	Fetal Brain Male	brain
14	chr4:3381000-3389200	Weak transcription	HSMMtube	muscle
15	chr4:3382600-3389000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:3382600-3389000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:3383200-3389600	Weak transcription	Fetal Brain Female	brain
18	chr4:3383600-3388000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:3384600-3387600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:3386200-3387200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr4:3386200-3387400	Flanking Active TSS	Liver	Liver
22	chr4:3386200-3387400	Enhancers	Stomach Mucosa	stomach
23	chr4:3386200-3387800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr4:3386200-3387800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:3386200-3387800	Enhancers	Right Ventricle	heart
26	chr4:3386200-3388000	Flanking Active TSS	HMEC	breast
27	chr4:3386200-3388000	Flanking Active TSS	NHEK	skin
28	chr4:3386200-3388200	Enhancers	Lung	lung
29	chr4:3386200-3388200	Flanking Active TSS	HepG2	liver
30	chr4:3386200-3390000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:3386200-3391400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr4:3386400-3387200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:3386400-3387200	Active TSS	Brain Substantia Nigra	brain
34	chr4:3386400-3387200	Flanking Active TSS	Fetal Intestine Large	intestine
35	chr4:3386400-3387200	Flanking Active TSS	Fetal Intestine Small	intestine
36	chr4:3386400-3387200	Active TSS	Rectal Smooth Muscle	rectum
37	chr4:3386400-3387400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:3386400-3387400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr4:3386400-3387400	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr4:3386400-3387400	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr4:3386400-3387400	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr4:3386400-3387600	Active TSS	Brain Hippocampus Middle	brain
43	chr4:3386400-3387600	Enhancers	Fetal Muscle Leg	muscle
44	chr4:3386400-3387800	Flanking Active TSS	Esophagus	oesophagus
45	chr4:3386400-3388000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:3386400-3388000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr4:3386400-3388000	Enhancers	NH-A	brain
48	chr4:3386400-3388200	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr4:3386400-3388200	Enhancers	Fetal Muscle Trunk	muscle
50	chr4:3386400-3388200	Enhancers	Spleen	Spleen

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