Variant report

Variant	rs16840683
Chromosome Location	chr2:209048821-209048822
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	chr2:209048730-209049260	SK-N-MC	brain:	n/a	n/a
2	FOXA1	chr2:209048540-209049013	HepG2	liver:	n/a	n/a
3	FOXA1	chr2:209048614-209048999	HepG2	liver:	n/a	n/a
4	FOXP2	chr2:209048709-209049124	SK-N-MC	brain:	n/a	n/a
5	FOXA2	chr2:209048659-209048890	HepG2	liver:	n/a	n/a
6	CEBPB	chr2:209048718-209048898	HepG2	liver:	n/a	chr2:209048819-209048830
7	CEBPB	chr2:209048683-209048969	HepG2	liver:	n/a	chr2:209048819-209048830
8	CEBPB	chr2:209048700-209048981	H1-hESC	embryonic stem cell:	n/a	chr2:209048819-209048830
9	HNF4A	chr2:209048707-209048902	HepG2	liver:	n/a	n/a
10	RAD21	chr2:209048325-209048901	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTBP2	chr2:209048380-209049301	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:209048413..209050423-chr2:209125192..209127904,2	K562	blood:
2	chr2:209045281..209046929-chr2:209048317..209050730,2	K562	blood:

Variant related genes	Relation type
C2orf80	TF binding region
ENSG00000188674	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10168933	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10932247	1.00[ASN][1000 genomes]
rs10932248	1.00[ASN][1000 genomes]
rs10932249	1.00[ASN][1000 genomes]
rs10932250	1.00[ASN][1000 genomes]
rs10932251	1.00[ASN][1000 genomes]
rs12373811	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs13027625	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13402685	1.00[ASN][1000 genomes]
rs13411179	0.80[EUR][1000 genomes]
rs13430046	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13432776	0.84[EUR][1000 genomes]
rs2028878	1.00[ASN][1000 genomes]
rs2197565	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4675738	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6435429	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6711758	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6714981	1.00[CHB][hapmap]
rs6740421	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6743514	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6755619	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs73065258	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73065286	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv834517	chr2:209006797-209170269	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv584298	chr2:209021232-209052303	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv584299	chr2:209021232-209067051	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv875749	chr2:209022909-209062388	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv875750	chr2:209022909-209069303	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv869592	chr2:209029861-209060862	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv584300	chr2:209033557-209054928	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv2763083	chr2:209033581-209058397	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv584301	chr2:209034715-209054928	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv875751	chr2:209042963-209110784	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS 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	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209040000-209064000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:209044200-209051400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:209047600-209049000	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr2:209047600-209049200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:209048000-209049600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr2:209048200-209049000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:209048200-209049000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:209048200-209049000	Enhancers	Fetal Brain Female	brain
9	chr2:209048200-209049400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:209048200-209049400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr2:209048200-209049600	Enhancers	Liver	Liver
12	chr2:209048200-209049800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:209048200-209050200	Enhancers	Brain Germinal Matrix	brain
14	chr2:209048200-209051200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:209048400-209049000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr2:209048400-209049000	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr2:209048400-209049200	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr2:209048400-209049200	Active TSS	H9 Cell Line	embryonic stem cell
19	chr2:209048400-209049200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr2:209048400-209049200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr2:209048400-209049200	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr2:209048400-209049200	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr2:209048400-209049200	Enhancers	Fetal Brain Male	brain
24	chr2:209048400-209049400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr2:209048400-209049600	Active TSS	Brain Cingulate Gyrus	brain
26	chr2:209048600-209049000	Active TSS	H1 Cell Line	embryonic stem cell
27	chr2:209048600-209049000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:209048600-209049000	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr2:209048600-209049000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:209048600-209051400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:209048800-209049000	Bivalent Enhancer	Primary B cells from cord blood	blood
32	chr2:209048800-209049000	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr2:209048800-209049000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr2:209048800-209049000	Bivalent Enhancer	Fetal Thymus	thymus
35	chr2:209048800-209049000	Enhancers	Ovary	ovary
36	chr2:209048800-209049000	Flanking Bivalent TSS/Enh	HepG2	liver
37	chr2:209048800-209049000	Bivalent Enhancer	NHEK	skin
38	chr2:209048800-209049200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:209048800-209049200	Enhancers	Primary B cells from peripheral blood	blood
40	chr2:209048800-209049200	Bivalent Enhancer	Fetal Lung	lung
41	chr2:209048800-209049200	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr2:209048800-209049400	Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr2:209048800-209049400	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr2:209048800-209049600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:209048800-209050200	Active TSS	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links