Variant report

Variant	rs12668532
Chromosome Location	chr7:56036983-56036984
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:56034331..56037104-chr7:56116413..56119304,2	K562	blood:
2	chr7:56031968..56033633-chr7:56035445..56039126,3	MCF-7	breast:
3	chr7:56035043..56037543-chr7:56067785..56069353,2	MCF-7	breast:
4	chr7:56030496..56032605-chr7:56035800..56038513,2	MCF-7	breast:
5	chr7:56036295..56037820-chr7:56154897..56156610,2	K562	blood:
6	chr7:56036722..56038681-chr7:56040095..56042469,2	MCF-7	breast:
7	chr7:56035559..56038065-chr7:56131631..56133555,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164776	Chromatin interaction
ENSG00000146733	Chromatin interaction
ENSG00000129103	Chromatin interaction
ENSG00000146729	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10265826	0.81[EUR][1000 genomes]
rs10274148	0.81[EUR][1000 genomes]
rs1059309	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1078650	0.96[ASN][1000 genomes]
rs10800	0.95[CEU][hapmap];0.82[CHD][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs1136390	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11974040	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12154231	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154781	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12155441	0.95[CEU][hapmap];0.84[CHD][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12532776	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12668504	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12669185	0.84[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12673255	0.95[CEU][hapmap];0.84[CHD][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs12674147	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12674334	0.90[ASN][1000 genomes]
rs13231257	0.94[ASN][1000 genomes]
rs2006649	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2289062	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2331095	0.91[ASN][1000 genomes]
rs28438587	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34795560	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34869068	0.91[ASN][1000 genomes]
rs35791463	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3813505	0.95[CEU][hapmap]
rs4424212	0.95[CEU][hapmap];0.86[CHD][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap]
rs55852201	0.89[ASN][1000 genomes]
rs55940597	0.81[EUR][1000 genomes]
rs58006921	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58981281	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59199266	0.83[ASN][1000 genomes]
rs59849749	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs60160896	0.94[ASN][1000 genomes]
rs60962915	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6593291	0.84[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.92[ASN][1000 genomes]
rs6947671	0.95[CEU][hapmap];0.82[CHD][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs6947853	0.84[ASN][1000 genomes]
rs6955639	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6960348	0.95[CEU][hapmap]
rs6970842	0.95[CEU][hapmap];0.84[CHD][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs6975697	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs73134780	0.95[ASN][1000 genomes]
rs73138774	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73138777	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7456530	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs7778601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7781165	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7793536	1.00[CEU][hapmap]
rs7795095	0.84[ASN][1000 genomes]
rs7798243	0.84[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.91[ASN][1000 genomes]
rs7804578	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking 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	84 gene(s)	inside rSNPs	diseases
5	nsv1019400	chr7:55709827-56094540	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers 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	46 gene(s)	inside rSNPs	diseases
6	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
7	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers 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	64 gene(s)	inside rSNPs	diseases
8	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
9	nsv888064	chr7:55831721-56104539	Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
11	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
12	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
13	nsv1034826	chr7:55962159-56092835	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	nsv1033225	chr7:55962159-56094540	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12668532	SUMF2	cis	cerebellum	SCAN
rs12668532	SUMF2	cis	parietal	SCAN
rs12668532	ZNF713	cis	cerebellum	SCAN
rs12668532	SUMF2	cis	multi-tissue	Pritchard
rs12668532	LOC378075	cis	multi-tissue	Pritchard
rs12668532	SUMF2	cis	Esophagus Muscularis	GTEx
rs12668532	ZNF713	cis	parietal	SCAN
rs12668532	SUMF2	cis	lymphoblastoid	seeQTL
rs12668532	LOC645317	trans	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56033000-56039200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:56033200-56045400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr7:56033200-56045600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:56033200-56045600	Weak transcription	Aorta	Aorta
5	chr7:56033200-56045800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr7:56033200-56048600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr7:56033200-56050400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:56033200-56081400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:56033400-56040400	Weak transcription	Small Intestine	intestine
10	chr7:56033400-56045200	Weak transcription	HUVEC	blood vessel
11	chr7:56033400-56045600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr7:56033400-56045600	Weak transcription	Primary B cells from peripheral blood	blood
13	chr7:56033400-56047000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr7:56033400-56047600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr7:56033600-56037800	Weak transcription	Primary B cells from cord blood	blood
16	chr7:56033600-56045600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr7:56033800-56037200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr7:56033800-56038200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr7:56033800-56038400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr7:56033800-56038400	Weak transcription	HSMMtube	muscle
21	chr7:56033800-56038600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:56033800-56038600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr7:56033800-56038600	Weak transcription	Stomach Mucosa	stomach
24	chr7:56033800-56039000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:56033800-56039400	Strong transcription	Fetal Intestine Small	intestine
26	chr7:56033800-56045400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr7:56033800-56045400	Weak transcription	Hela-S3	cervix
28	chr7:56033800-56045400	Weak transcription	HSMM	muscle
29	chr7:56033800-56045600	Weak transcription	Placenta	Placenta
30	chr7:56033800-56045800	Weak transcription	Fetal Thymus	thymus
31	chr7:56033800-56045800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr7:56033800-56046000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr7:56033800-56046800	Weak transcription	GM12878-XiMat	blood
34	chr7:56033800-56046800	Weak transcription	NHLF	lung
35	chr7:56033800-56047200	Weak transcription	Colonic Mucosa	Colon
36	chr7:56033800-56047800	Weak transcription	HMEC	breast
37	chr7:56033800-56063000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr7:56033800-56065800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr7:56034000-56037000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr7:56034000-56037000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr7:56034000-56038200	Weak transcription	Brain Angular Gyrus	brain
42	chr7:56034000-56038400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr7:56034000-56038400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr7:56034000-56038400	Weak transcription	Brain Anterior Caudate	brain
45	chr7:56034000-56038400	Enhancers	Fetal Heart	heart
46	chr7:56034000-56038600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr7:56034000-56038800	Weak transcription	NH-A	brain
48	chr7:56034000-56045400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr7:56034000-56045400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr7:56034000-56045600	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links