Variant report

Variant	rs12592342
Chromosome Location	chr15:31749336-31749337
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	NR3C1	chr15:31748696-31749357	A549	lung:	n/a	n/a
2	FOXA2	chr15:31749027-31749513	A549	lung:	n/a	n/a
3	BCL3	chr15:31749134-31749475	GM12878	blood:	n/a	n/a
4	FOSL2	chr15:31749161-31750248	A549	lung:	n/a	chr15:31749997-31750005 chr15:31749995-31750007
5	BCL3	chr15:31749116-31749537	GM12878	blood:	n/a	n/a
6	SP1	chr15:31748963-31750246	A549	lung:	n/a	n/a
7	MAX	chr15:31749192-31750190	A549	lung:	n/a	chr15:31749603-31749616 chr15:31749605-31749614 chr15:31749600-31749619 chr15:31749604-31749615
8	MAX	chr15:31749019-31750228	A549	lung:	n/a	chr15:31749603-31749616 chr15:31749605-31749614 chr15:31749600-31749619 chr15:31749604-31749615
9	TCF12	chr15:31749042-31750243	A549	lung:	n/a	chr15:31750160-31750167
10	FOXA2	chr15:31749007-31749540	A549	lung:	n/a	n/a
11	MYC	chr15:31749306-31750073	MCF10A-Er-Src	breast:	n/a	chr15:31749603-31749616 chr15:31749605-31749614 chr15:31749600-31749619 chr15:31749604-31749615

No.	Distal block	Cell Line	Cell type
1	chr15:31747904..31750478-chr15:31754531..31757245,2	MCF-7	breast:
2	chr15:31748477..31753108-chr15:31776889..31783172,7	MCF-7	breast:
3	chr15:31731861..31735385-chr15:31748681..31751856,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259696	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1077169	0.94[ASN][1000 genomes]
rs10851568	0.94[ASN][1000 genomes]
rs10851569	0.94[ASN][1000 genomes]
rs11071070	0.94[ASN][1000 genomes]
rs11071075	0.94[ASN][1000 genomes]
rs11071076	0.93[ASN][1000 genomes]
rs12148161	0.93[ASN][1000 genomes]
rs12148181	0.94[ASN][1000 genomes]
rs12439195	0.94[ASN][1000 genomes]
rs12439214	0.93[ASN][1000 genomes]
rs12439216	0.93[ASN][1000 genomes]
rs12440316	0.94[ASN][1000 genomes]
rs12441399	0.82[ASN][1000 genomes]
rs12441529	0.94[ASN][1000 genomes]
rs12441571	0.82[ASN][1000 genomes]
rs12443255	0.94[ASN][1000 genomes]
rs12443432	0.94[ASN][1000 genomes]
rs12592099	0.93[ASN][1000 genomes]
rs12592371	0.96[ASN][1000 genomes]
rs12592652	0.87[MEX][hapmap]
rs12595455	0.96[ASN][1000 genomes]
rs1380235	0.96[ASN][1000 genomes]
rs17228303	0.96[ASN][1000 genomes]
rs17228317	0.92[ASN][1000 genomes]
rs17815977	0.94[ASN][1000 genomes]
rs2008020	0.92[ASN][1000 genomes]
rs2125617	0.94[ASN][1000 genomes]
rs2125618	0.94[ASN][1000 genomes]
rs2219508	1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2338683	0.94[ASN][1000 genomes]
rs28366602	0.94[ASN][1000 genomes]
rs28367155	0.96[ASN][1000 genomes]
rs28379435	0.94[ASN][1000 genomes]
rs28392564	0.94[ASN][1000 genomes]
rs28403178	0.93[ASN][1000 genomes]
rs28421719	0.96[ASN][1000 genomes]
rs28470561	0.94[ASN][1000 genomes]
rs28533482	0.94[ASN][1000 genomes]
rs28549906	0.93[ASN][1000 genomes]
rs28557161	0.94[ASN][1000 genomes]
rs28579624	0.96[ASN][1000 genomes]
rs28619436	0.96[ASN][1000 genomes]
rs28623261	0.94[ASN][1000 genomes]
rs28633343	0.96[ASN][1000 genomes]
rs28633823	0.94[ASN][1000 genomes]
rs28644187	0.96[ASN][1000 genomes]
rs28655541	0.94[ASN][1000 genomes]
rs28668028	0.94[ASN][1000 genomes]
rs28673491	0.94[ASN][1000 genomes]
rs28683761	0.94[ASN][1000 genomes]
rs28685794	0.96[ASN][1000 genomes]
rs28687203	0.94[ASN][1000 genomes]
rs28696791	0.93[ASN][1000 genomes]
rs28703622	0.94[ASN][1000 genomes]
rs28716634	0.96[ASN][1000 genomes]
rs28825540	0.85[ASN][1000 genomes]
rs28896251	0.93[ASN][1000 genomes]
rs35643888	0.89[ASN][1000 genomes]
rs4238555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4401013	0.84[ASN][1000 genomes]
rs4414458	0.81[ASN][1000 genomes]
rs4451913	0.82[ASN][1000 genomes]
rs4497646	0.92[ASN][1000 genomes]
rs4611410	0.87[ASN][1000 genomes]
rs4779528	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4779529	0.96[ASN][1000 genomes]
rs4779530	0.96[ASN][1000 genomes]
rs4779531	0.94[ASN][1000 genomes]
rs4779881	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55806858	0.94[ASN][1000 genomes]
rs56008248	0.94[ASN][1000 genomes]
rs56332002	0.96[ASN][1000 genomes]
rs56349550	0.94[ASN][1000 genomes]
rs62037907	0.96[ASN][1000 genomes]
rs7403275	0.95[ASN][1000 genomes]
rs7403458	0.96[ASN][1000 genomes]
rs755809	0.93[ASN][1000 genomes]
rs755812	0.93[ASN][1000 genomes]
rs8023660	0.94[ASN][1000 genomes]
rs8023664	0.94[ASN][1000 genomes]
rs8023790	0.94[ASN][1000 genomes]
rs8035018	0.94[ASN][1000 genomes]
rs8038667	0.96[ASN][1000 genomes]
rs8038953	0.94[ASN][1000 genomes]
rs8040186	0.94[ASN][1000 genomes]
rs971330	0.96[ASN][1000 genomes]
rs971331	0.96[ASN][1000 genomes]
rs971332	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv903840	chr15:31589970-31800149	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1051589	chr15:31728004-31972706	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv542320	chr15:31728004-31972706	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv469633	chr15:31731003-31904613	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv482330	chr15:31731003-31904613	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv903844	chr15:31736091-31781988	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1046271	chr15:31741255-31795961	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12592342	KLF13	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31734400-31750000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:31741400-31749400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:31745800-31750000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:31747000-31750800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr15:31748000-31749600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr15:31748000-31751000	Weak transcription	Primary T cells from cord blood	blood
7	chr15:31748000-31751000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:31748200-31750400	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr15:31748200-31750800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr15:31748200-31750800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr15:31748200-31750800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:31748200-31751000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr15:31748200-31751000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr15:31748400-31751800	Enhancers	A549	lung
15	chr15:31748600-31751600	Enhancers	Esophagus	oesophagus
16	chr15:31748600-31751800	Enhancers	NHEK	skin
17	chr15:31748600-31752000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:31748800-31749400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:31748800-31749400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:31748800-31749400	Enhancers	Aorta	Aorta
21	chr15:31748800-31749400	Enhancers	NHDF-Ad	bronchial
22	chr15:31748800-31750600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:31748800-31750600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:31748800-31750800	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr15:31748800-31751000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:31748800-31751000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr15:31748800-31751200	Enhancers	Adipose Nuclei	Adipose
28	chr15:31748800-31751400	Enhancers	HSMM	muscle
29	chr15:31748800-31751400	Enhancers	HSMMtube	muscle
30	chr15:31749000-31749600	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr15:31749000-31749800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:31749000-31750000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr15:31749000-31750400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr15:31749000-31750600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
35	chr15:31749000-31750600	Bivalent Enhancer	Fetal Muscle Leg	muscle
36	chr15:31749000-31750600	Enhancers	NHLF	lung
37	chr15:31749000-31751800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:31749200-31749400	Flanking Active TSS	Osteobl	bone
39	chr15:31749200-31749800	Bivalent Enhancer	HUVEC	blood vessel
40	chr15:31749200-31750200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:31749200-31750200	Enhancers	Muscle Satellite Cultured Cells	--
42	chr15:31749200-31750400	Enhancers	GM12878-XiMat	blood
43	chr15:31749200-31750600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr15:31749200-31751400	Enhancers	NH-A	brain
45	chr15:31749200-31752000	Enhancers	HMEC	breast
46	chr15:31749200-31753200	Weak transcription	Left Ventricle	heart
47	chr15:31749200-31764000	Weak transcription	Right Atrium	heart

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