Variant report

Variant	rs16972776
Chromosome Location	chr15:42452013-42452014
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:42449741-42452236	K562	blood:	n/a	n/a
2	POLR2A	chr15:42451588-42452157	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr15:42451743-42452108	GM12891	blood:	n/a	n/a
4	POLR2A	chr15:42451974-42452171	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:42451110..42452642-chr15:42456255..42457844,2	K562	blood:
2	chr15:42442020..42443791-chr15:42450046..42452930,2	K562	blood:
3	chr15:42449739..42452702-chr15:42454816..42457885,4	K562	blood:
4	chr15:42450192..42452285-chr15:42459355..42462158,2	K562	blood:
5	chr15:42441690..42443791-chr15:42450046..42452930,3	K562	blood:

No data

Variant related genes	Relation type
PLA2G4F	TF binding region
ENSG00000166887	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10220859	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes]
rs12440087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs12441642	0.85[CHB][hapmap]
rs1624183	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1659213	1.00[CEU][hapmap]
rs1659218	1.00[CEU][hapmap]
rs1659219	1.00[CEU][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs1659222	1.00[CEU][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs1678992	1.00[CEU][hapmap]
rs16972770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16972779	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap]
rs16972887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes]
rs16973008	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes]
rs16973045	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes]
rs16973060	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1703754	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2138831	0.85[CHB][hapmap];0.92[CHD][hapmap]
rs2412688	1.00[CHB][hapmap]
rs2620386	1.00[CEU][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes]
rs2918460	1.00[CEU][hapmap]
rs3743005	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs3743007	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs3743008	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs3825785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs4506867	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4923932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4923945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs4924627	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4924630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs4924631	0.83[EUR][1000 genomes]
rs4924644	0.81[AMR][1000 genomes]
rs4924672	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs4924673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs55882551	0.81[AMR][1000 genomes]
rs56257215	0.82[AMR][1000 genomes]
rs56670003	0.85[AMR][1000 genomes]
rs56987883	0.85[AMR][1000 genomes]
rs57393446	0.85[AMR][1000 genomes]
rs57973092	0.82[AMR][1000 genomes]
rs58292736	0.85[AMR][1000 genomes]
rs58712370	0.82[AMR][1000 genomes]
rs59094161	0.82[AMR][1000 genomes]
rs59138723	0.81[AMR][1000 genomes]
rs59320762	0.82[AMR][1000 genomes]
rs59974698	0.86[AMR][1000 genomes]
rs60486546	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60506946	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61133768	0.82[AMR][1000 genomes]
rs622714	0.90[EUR][1000 genomes]
rs624841	0.90[EUR][1000 genomes]
rs678778	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs681029	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7179203	0.82[AMR][1000 genomes]
rs7179709	1.00[CEU][hapmap]
rs7180279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs7181979	0.83[EUR][1000 genomes]
rs73398938	0.85[AMR][1000 genomes]
rs73402707	0.82[AMR][1000 genomes]
rs73403545	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73403546	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73403548	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73403550	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73407403	0.86[AMR][1000 genomes]
rs74009020	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025601	0.85[CHB][hapmap]
rs8041951	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers 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 miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv9245	chr15:42441849-42453572	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42448200-42453000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr15:42448400-42452400	Weak transcription	Fetal Kidney	kidney
3	chr15:42448600-42452800	Weak transcription	Hela-S3	cervix
4	chr15:42448600-42453800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:42448800-42452200	Weak transcription	Small Intestine	intestine
6	chr15:42449000-42452200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr15:42449000-42452400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:42449000-42481800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:42449200-42452400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:42449200-42453800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:42449200-42456000	Weak transcription	Stomach Mucosa	stomach
12	chr15:42449600-42452200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr15:42449600-42468200	Strong transcription	Fetal Brain Female	brain
14	chr15:42449800-42452200	Enhancers	Left Ventricle	heart
15	chr15:42450200-42468600	Strong transcription	Fetal Stomach	stomach
16	chr15:42450200-42472400	Strong transcription	Fetal Intestine Small	intestine
17	chr15:42450400-42452200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr15:42450400-42457000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:42450400-42468400	Strong transcription	Primary T cells from cord blood	blood
20	chr15:42450400-42468400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr15:42450400-42476600	Strong transcription	Fetal Muscle Leg	muscle
22	chr15:42450600-42452800	Enhancers	Fetal Heart	heart
23	chr15:42450600-42457400	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr15:42450600-42460800	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr15:42450600-42463400	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr15:42450600-42468000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:42450600-42468200	Strong transcription	Brain Germinal Matrix	brain
28	chr15:42450600-42479800	Weak transcription	Psoas Muscle	Psoas
29	chr15:42450600-42485000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:42450600-42486200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:42450600-42487400	Strong transcription	Primary B cells from cord blood	blood
32	chr15:42450800-42463400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr15:42450800-42471400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr15:42450800-42484000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr15:42450800-42485000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr15:42450800-42485200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr15:42451000-42452200	Genic enhancers	Lung	lung
38	chr15:42451000-42452200	Enhancers	Right Atrium	heart
39	chr15:42451000-42452400	Genic enhancers	Stomach Smooth Muscle	stomach
40	chr15:42451000-42452600	Genic enhancers	Right Ventricle	heart
41	chr15:42451000-42452800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr15:42451000-42452800	Weak transcription	Fetal Brain Male	brain
43	chr15:42451000-42452800	Strong transcription	A549	lung
44	chr15:42451000-42460800	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr15:42451000-42460800	Strong transcription	HepG2	liver
46	chr15:42451000-42461000	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr15:42451000-42461000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr15:42451000-42461200	Strong transcription	Gastric	stomach
49	chr15:42451000-42461200	Strong transcription	Spleen	Spleen
50	chr15:42451000-42462000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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