Variant report

Variant	rs16956460
Chromosome Location	chr15:31317445-31317446
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	GATA3	chr15:31317329-31317604	T-47D	breast:	n/a	chr15:31317461-31317470
2	GATA3	chr15:31316340-31317869	SK-N-SH	brain:	n/a	chr15:31317461-31317470 chr15:31316560-31316568 chr15:31316630-31316639
3	MAZ	chr15:31316336-31317662	IMR90	lung:	n/a	n/a
4	GATA3	chr15:31316290-31317779	SK-N-SH	brain:	n/a	chr15:31317461-31317470 chr15:31316560-31316568 chr15:31316630-31316639
5	CEBPB	chr15:31316515-31317481	IMR90	lung:	n/a	n/a
6	POLR2A	chr15:31317249-31317585	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr15:31317248-31317783	SH-SY5Y	brain:	n/a	chr15:31317461-31317470
8	TCF12	chr15:31316288-31317836	SK-N-SH	brain:	n/a	chr15:31316555-31316562
9	CTCF	chr15:31317360-31317510	AG04449	skin:	n/a	n/a
10	GATA2	chr15:31316282-31317710	HUVEC	blood vessel:	n/a	chr15:31317461-31317470 chr15:31316560-31316568 chr15:31316630-31316639
11	KAP1	chr15:31317129-31317625	U2OS	brain:	n/a	n/a
12	GATA3	chr15:31316446-31317635	A549	lung:	n/a	chr15:31317461-31317470 chr15:31316560-31316568 chr15:31316630-31316639
13	GATA2	chr15:31317222-31317766	SH-SY5Y	brain:	n/a	chr15:31317461-31317470
14	TCF12	chr15:31316328-31317749	SK-N-SH	brain:	n/a	chr15:31316555-31316562

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31316162..31318225-chr15:31318873..31321784,2	K562	blood:

Variant related genes	Relation type
ENSG00000259720	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10519726	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12437677	0.93[ASN][1000 genomes]
rs12441456	0.91[ASN][1000 genomes]
rs12442021	0.89[ASN][1000 genomes]
rs12442333	0.91[ASN][1000 genomes]
rs12442823	0.93[ASN][1000 genomes]
rs16956414	0.89[ASN][1000 genomes]
rs16956422	0.87[ASN][1000 genomes]
rs28487996	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36042462	0.91[ASN][1000 genomes]
rs3743232	0.93[ASN][1000 genomes]
rs3784588	0.93[ASN][1000 genomes]
rs6493358	0.85[ASN][1000 genomes]
rs7175354	0.93[ASN][1000 genomes]
rs73368444	0.91[ASN][1000 genomes]
rs872843	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv916936	chr15:30921917-31337510	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv525795	chr15:30936285-31324531	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS 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	35 gene(s)	inside rSNPs	diseases
4	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
8	esv33507	chr15:31183324-31471023	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers 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	35 gene(s)	inside rSNPs	diseases
9	nsv832952	chr15:31204426-31333998	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv1052722	chr15:31261834-31609680	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
11	nsv542315	chr15:31261834-31609680	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
12	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
13	nsv903835	chr15:31312743-31384797	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31311000-31319600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:31313600-31317800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr15:31314800-31317600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:31314800-31318600	Enhancers	Placenta	Placenta
5	chr15:31315000-31317600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:31315000-31318000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:31315200-31317600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr15:31315200-31317600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:31315200-31317800	Enhancers	Fetal Kidney	kidney
10	chr15:31315200-31317800	Enhancers	NHLF	lung
11	chr15:31315400-31317800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr15:31315400-31318400	Enhancers	H1 Cell Line	embryonic stem cell
13	chr15:31315400-31318600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:31315600-31317600	Enhancers	H9 Cell Line	embryonic stem cell
15	chr15:31315600-31317600	Enhancers	HSMM	muscle
16	chr15:31315600-31317800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:31315600-31317800	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr15:31315600-31317800	Enhancers	NH-A	brain
19	chr15:31315600-31320400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:31315800-31317600	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr15:31315800-31317600	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr15:31315800-31317800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:31315800-31319400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr15:31316000-31317600	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr15:31316000-31317600	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr15:31316200-31317800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr15:31316200-31317800	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr15:31316200-31318400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:31316400-31324800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:31316600-31317600	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr15:31316600-31317600	Flanking Active TSS	HepG2	liver
32	chr15:31316600-31317800	Enhancers	Fetal Intestine Small	intestine
33	chr15:31316600-31317800	Enhancers	HMEC	breast
34	chr15:31316600-31318200	Enhancers	Fetal Intestine Large	intestine
35	chr15:31316600-31318200	Enhancers	HUVEC	blood vessel
36	chr15:31316800-31330000	Weak transcription	Pancreas	Pancrea
37	chr15:31317000-31317600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:31317200-31317600	Enhancers	Muscle Satellite Cultured Cells	--
39	chr15:31317200-31317600	Enhancers	A549	lung
40	chr15:31317200-31317800	Enhancers	NHEK	skin
41	chr15:31317400-31317800	Enhancers	Osteobl	bone
42	chr15:31317400-31318200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:31317400-31319600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr15:31317400-31323400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr15:31317400-31323800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr15:31317400-31326600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr15:31317400-31328400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr15:31317400-31334200	Weak transcription	Gastric	stomach

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