Variant report

Variant	rs28372932
Chromosome Location	chr16:31339625-31339626
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	SUZ12	chr16:31339602-31340438	H1-hESC	embryonic stem cell:	n/a	n/a
2	GTF2F1	chr16:31339619-31339640	H1-hESC	embryonic stem cell:	n/a	n/a
3	TCF7L2	chr16:31339589-31339741	Hela-S3	cervix:	n/a	n/a
4	BCL3	chr16:31339512-31340343	GM12878	blood:	n/a	n/a
5	MAX	chr16:31339411-31339907	NB4	blood:	n/a	n/a
6	NFATC1	chr16:31339558-31340382	GM12878	blood:	n/a	n/a
7	SIN3A	chr16:31339254-31339711	H1-hESC	embryonic stem cell:	n/a	n/a
8	BCL3	chr16:31339430-31340482	GM12878	blood:	n/a	n/a
9	NR2C2	chr16:31339597-31340368	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COX6A2-5	chr16:31338997-31340036	NONHSAT141893

Variant related genes	Relation type
ITGAM	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10747210	0.87[ASN][1000 genomes]
rs10782004	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11150610	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11150611	0.88[ASN][1000 genomes]
rs11150612	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11150613	0.88[ASN][1000 genomes]
rs11150617	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11150619	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1143682	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11574630	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11574631	0.87[ASN][1000 genomes]
rs11641202	0.96[ASN][1000 genomes]
rs11642120	0.92[ASN][1000 genomes]
rs11645917	0.89[ASN][1000 genomes]
rs11859274	0.89[ASN][1000 genomes]
rs11863627	0.95[ASN][1000 genomes]
rs12444713	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12597154	0.89[ASN][1000 genomes]
rs12600286	0.83[ASN][1000 genomes]
rs12923297	0.89[ASN][1000 genomes]
rs12935192	0.89[ASN][1000 genomes]
rs13338928	0.98[ASN][1000 genomes]
rs2230429	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3087796	0.96[ASN][1000 genomes]
rs36100148	0.97[ASN][1000 genomes]
rs3925074	0.94[ASN][1000 genomes]
rs3925075	0.94[ASN][1000 genomes]
rs4075052	0.93[ASN][1000 genomes]
rs4077810	0.97[ASN][1000 genomes]
rs41440449	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4261553	0.93[ASN][1000 genomes]
rs4280256	0.80[ASN][1000 genomes]
rs4359460	0.93[ASN][1000 genomes]
rs4411512	0.93[ASN][1000 genomes]
rs4448960	0.94[ASN][1000 genomes]
rs4450409	0.85[ASN][1000 genomes]
rs4459557	0.88[ASN][1000 genomes]
rs4493054	0.87[ASN][1000 genomes]
rs4506917	0.94[ASN][1000 genomes]
rs4594268	0.92[ASN][1000 genomes]
rs4597342	0.95[ASN][1000 genomes]
rs4608351	0.93[ASN][1000 genomes]
rs4889543	0.99[ASN][1000 genomes]
rs4889647	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4889649	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55742763	0.99[ASN][1000 genomes]
rs56392848	0.88[ASN][1000 genomes]
rs57202326	0.86[ASN][1000 genomes]
rs59338016	0.89[ASN][1000 genomes]
rs61194152	0.88[ASN][1000 genomes]
rs62051517	0.97[ASN][1000 genomes]
rs7192161	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7192375	0.98[ASN][1000 genomes]
rs7195915	0.97[ASN][1000 genomes]
rs7195945	0.97[ASN][1000 genomes]
rs7206295	0.91[ASN][1000 genomes]
rs7501207	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8052324	0.97[ASN][1000 genomes]
rs8058882	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8060268	0.97[ASN][1000 genomes]
rs8062159	0.86[ASN][1000 genomes]
rs9673398	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9673404	0.92[ASN][1000 genomes]
rs9673405	0.94[ASN][1000 genomes]
rs9673519	0.93[ASN][1000 genomes]
rs9673522	0.94[ASN][1000 genomes]
rs9674009	0.94[ASN][1000 genomes]
rs9888907	0.93[ASN][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	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
2	nsv1059459	chr16:31299088-31462251	Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv542901	chr16:31299088-31462251	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
5	nsv1058992	chr16:31337455-31414881	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv542902	chr16:31337455-31414881	Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv1061980	chr16:31338462-31415471	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31323000-31344600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr16:31331800-31342000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr16:31332200-31342000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr16:31333600-31342400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr16:31333800-31342400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr16:31335200-31341800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr16:31335800-31342000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr16:31337000-31340800	Weak transcription	Placenta	Placenta
9	chr16:31338200-31340200	Strong transcription	Primary B cells from cord blood	blood
10	chr16:31338400-31342600	Weak transcription	Gastric	stomach
11	chr16:31338800-31342000	Strong transcription	Spleen	Spleen
12	chr16:31339000-31340000	Enhancers	GM12878-XiMat	blood
13	chr16:31339000-31340200	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr16:31339000-31340200	Enhancers	Dnd41	blood
15	chr16:31339200-31339800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr16:31339200-31340000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr16:31339200-31340000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr16:31339400-31339800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr16:31339400-31339800	Flanking Active TSS	Fetal Thymus	thymus
20	chr16:31339400-31339800	Flanking Active TSS	Thymus	Thymus
21	chr16:31339400-31340000	Enhancers	K562	blood
22	chr16:31339400-31340200	Enhancers	Primary hematopoietic stem cells	blood
23	chr16:31339600-31339800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr16:31339600-31339800	Enhancers	H9 Cell Line	embryonic stem cell
25	chr16:31339600-31339800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
26	chr16:31339600-31339800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr16:31339600-31340000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
28	chr16:31339600-31340000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr16:31339600-31340800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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