Variant report

Variant	rs16942777
Chromosome Location	chr17:46719690-46719691
allele	A/G
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	CTCF	chr17:46719560-46719710	GM12866	blood:	n/a	n/a
2	POLR2A	chr17:46719602-46719708	MCF-7	breast:	n/a	n/a
3	CTBP2	chr17:46719082-46720631	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr17:46719560-46719710	HUVEC	blood vessel:	n/a	n/a
5	SUZ12	chr17:46718975-46720971	H1-hESC	embryonic stem cell:	n/a	n/a
6	BCL3	chr17:46719673-46720482	A549	lung:	n/a	chr17:46720187-46720196
7	CTCF	chr17:46719681-46720054	H1-hESC	embryonic stem cell:	n/a	chr17:46719887-46719903
8	E2F6	chr17:46719670-46720609	A549	lung:	n/a	chr17:46719902-46719916
9	MAX	chr17:46719590-46720708	A549	lung:	n/a	n/a
10	CREB1	chr17:46719684-46720281	A549	lung:	n/a	n/a
11	JUND	chr17:46719686-46720296	A549	lung:	n/a	n/a
12	RAD21	chr17:46719657-46720150	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46713764..46716480-chr17:46718018..46720395,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272763	TF binding region
ENSG00000272763	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11079831	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16942817	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303489	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3096645	0.89[CEU][hapmap];0.80[ASN][1000 genomes]
rs3096646	0.81[CHB][hapmap]
rs3744774	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3809776	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3809777	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs3809778	0.83[ASN][1000 genomes]
rs3826540	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3826541	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4619445	0.87[ASN][1000 genomes]
rs73985889	0.85[ASN][1000 genomes]
rs73985890	0.81[ASN][1000 genomes]
rs7405887	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs881012	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8844	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs890433	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs890434	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases
2	nsv908579	chr17:46592413-46727289	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
3	nsv532113	chr17:46598247-47588570	Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	453 gene(s)	inside rSNPs	diseases
4	esv2758459	chr17:46602673-46836837	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
5	esv2758694	chr17:46602673-46836837	Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
6	nsv908581	chr17:46610646-46735520	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
7	nsv833471	chr17:46617787-46783345	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	356 gene(s)	inside rSNPs	diseases
8	nsv908584	chr17:46618926-46735520	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
9	nsv543380	chr17:46686151-46721371	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46717600-46720600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr17:46718600-46720000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:46718800-46720200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
4	chr17:46718800-46720800	Weak transcription	K562	blood
5	chr17:46719000-46719800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
6	chr17:46719000-46720000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr17:46719000-46720000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
8	chr17:46719000-46720000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
9	chr17:46719000-46720000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
10	chr17:46719000-46720200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
11	chr17:46719000-46720200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr17:46719000-46720200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr17:46719000-46720200	Bivalent Enhancer	Placenta	Placenta
14	chr17:46719200-46720000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
15	chr17:46719200-46720000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
16	chr17:46719200-46720000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr17:46719200-46720200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
18	chr17:46719200-46720200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
19	chr17:46719200-46720400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
20	chr17:46719200-46720400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr17:46719200-46720400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
22	chr17:46719200-46720400	Enhancers	Pancreas	Pancrea
23	chr17:46719200-46721200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
24	chr17:46719200-46721400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr17:46719200-46721400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
26	chr17:46719400-46719800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
27	chr17:46719400-46720200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
28	chr17:46719400-46720200	Bivalent/Poised TSS	Small Intestine	intestine
29	chr17:46719600-46719800	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
30	chr17:46719600-46719800	Bivalent Enhancer	Primary T cells from cord blood	blood
31	chr17:46719600-46719800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
32	chr17:46719600-46719800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr17:46719600-46719800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr17:46719600-46719800	Bivalent Enhancer	Fetal Stomach	stomach
35	chr17:46719600-46720000	Flanking Bivalent TSS/Enh	Sigmoid Colon	Sigmoid Colon
36	chr17:46719600-46720000	Bivalent Enhancer	Spleen	Spleen
37	chr17:46719600-46720200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr17:46719600-46720200	Transcr. at gene 5' and 3'	A549	lung
39	chr17:46719600-46720400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
40	chr17:46719600-46720400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr17:46719600-46720400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
42	chr17:46719600-46721600	Bivalent Enhancer	Adipose Nuclei	Adipose

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