Variant report

Variant	rs12925877
Chromosome Location	chr16:47351643-47351644
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	EP300	chr16:47351488-47352214	GM12878	blood:	n/a	n/a
2	EBF1	chr16:47351604-47352002	GM12878	blood:	n/a	chr16:47351779-47351790
3	CHD2	chr16:47351520-47352110	GM12878	blood:	n/a	n/a
4	NFATC1	chr16:47351624-47352271	GM12878	blood:	n/a	n/a
5	RCOR1	chr16:47351491-47352156	GM12878	blood:	n/a	n/a
6	CREB1	chr16:47351599-47352111	GM12878	blood:	n/a	n/a
7	RUNX3	chr16:47351280-47351670	GM12878	blood:	n/a	n/a
8	POLR2A	chr16:47351462-47351688	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:47343363..47345915-chr16:47349595..47352299,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PHKB-1	chr16:47351460-47351725	ENSG00000261369.1

Variant related genes	Relation type
ENSG00000222767	TF binding region
ENSG00000129636	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12051064	0.81[EUR][1000 genomes]
rs17811434	0.84[AMR][1000 genomes]
rs2058769	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34535698	0.84[AMR][1000 genomes]
rs7200665	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795199	chr16:47111119-47732476	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv1803802	chr16:47115776-47367144	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1059763	chr16:47147194-47373834	ZNF genes & repeats Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv916572	chr16:47227786-47646103	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv933151	chr16:47236330-47646103	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	esv2757637	chr16:47261512-47595005	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	esv2758644	chr16:47261512-47606287	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv1060396	chr16:47264261-47469345	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv428656	chr16:47316866-47469918	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv2758423	chr16:47316866-47606287	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv427983	chr16:47316866-47606287	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:47311400-47362200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr16:47318000-47354200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr16:47333400-47371600	Weak transcription	Esophagus	oesophagus
4	chr16:47333600-47354600	Weak transcription	HSMMtube	muscle
5	chr16:47334000-47354600	Weak transcription	HSMM	muscle
6	chr16:47334400-47355200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr16:47334400-47357000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr16:47334400-47357400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr16:47334400-47371200	Weak transcription	Aorta	Aorta
10	chr16:47334400-47371600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr16:47334400-47371600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr16:47334600-47354000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr16:47334600-47372800	Weak transcription	Primary T cells from cord blood	blood
14	chr16:47342800-47354400	Weak transcription	NHDF-Ad	bronchial
15	chr16:47342800-47364800	Weak transcription	Primary B cells from cord blood	blood
16	chr16:47344600-47371600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr16:47344800-47354600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr16:47344800-47358800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr16:47344800-47370200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr16:47345200-47357600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr16:47345800-47354400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr16:47346200-47371600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr16:47346400-47351800	Weak transcription	GM12878-XiMat	blood
24	chr16:47346400-47371400	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr16:47346400-47371400	Weak transcription	Dnd41	blood
26	chr16:47346400-47371400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr16:47346800-47371600	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr16:47348800-47352200	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr16:47350000-47352200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr16:47350200-47351800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr16:47350200-47352400	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr16:47350400-47351800	Enhancers	Brain Angular Gyrus	brain
33	chr16:47350400-47351800	Enhancers	Brain Hippocampus Middle	brain
34	chr16:47350400-47352200	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr16:47350600-47371000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr16:47351000-47351800	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr16:47351000-47354200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr16:47351400-47351800	Enhancers	Psoas Muscle	Psoas
39	chr16:47351400-47352200	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr16:47351400-47352200	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr16:47351400-47370200	Weak transcription	Ovary	ovary
42	chr16:47351600-47351800	Enhancers	H9 Cell Line	embryonic stem cell
43	chr16:47351600-47351800	Enhancers	Fetal Kidney	kidney
44	chr16:47351600-47352000	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links