Variant report

Variant	rs6460967
Chromosome Location	chr7:12611252-12611253
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	SUZ12	chr7:12609858-12611660	NT2-D1	testis:	n/a	n/a

Variant related genes	Relation type
ENSG00000225606	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10233337	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10248988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10255606	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10276226	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1129315	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17283514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17283696	0.95[JPT][hapmap]
rs1859989	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1859990	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1990223	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1990224	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1990225	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2215063	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240571	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240574	0.96[CEU][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes]
rs2240575	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3173628	1.00[CEU][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs3735221	0.91[EUR][1000 genomes]
rs3807863	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41379149	0.92[CEU][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes]
rs4361677	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55999874	0.83[AMR][1000 genomes]
rs6460965	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs6460968	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6954111	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs6954578	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6972418	0.80[AMR][1000 genomes]
rs6972477	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73060686	0.80[AMR][1000 genomes]
rs73293093	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7801351	0.88[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7811582	0.96[CEU][hapmap];0.83[TSI][hapmap]
rs968792	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv1021371	chr7:12530491-12710429	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1017577	chr7:12530491-12722947	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1030764	chr7:12532287-12710429	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv528031	chr7:12536336-12618764	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1025397	chr7:12543161-12612059	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1025006	chr7:12543161-12618924	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1027831	chr7:12543161-12619740	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv470066	chr7:12543794-12618764	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1033478	chr7:12547121-12618924	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv464379	chr7:12572742-12618764	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv606231	chr7:12572742-12618764	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1018053	chr7:12580554-12632996	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv1020242	chr7:12605593-12641202	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6460967	SCIN	Cis_1M	lymphoblastoid	RTeQTL
rs6460967	SOSTDC1	cis	cerebellum	SCAN
rs6460967	SCIN	cis	parietal	SCAN
rs6460967	SCIN	cis	Thyroid	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12609400-12611600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr7:12609600-12612000	Active TSS	Brain Anterior Caudate	brain
3	chr7:12609800-12611600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr7:12610200-12611600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr7:12610200-12612000	Active TSS	Rectal Mucosa Donor 31	rectum
6	chr7:12610200-12612600	Bivalent/Poised TSS	Fetal Kidney	kidney
7	chr7:12610400-12613400	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr7:12610800-12611400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:12610800-12611600	Active TSS	Lung	lung
10	chr7:12610800-12611800	Active TSS	Colonic Mucosa	Colon
11	chr7:12611000-12611400	Bivalent/Poised TSS	Fetal Stomach	stomach
12	chr7:12611000-12611600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:12611000-12611600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr7:12611000-12611600	Active TSS	Gastric	stomach
15	chr7:12611000-12611800	Active TSS	Stomach Mucosa	stomach
16	chr7:12611000-12612800	Weak transcription	K562	blood
17	chr7:12611000-12613200	Active TSS	Duodenum Mucosa	Duodenum
18	chr7:12611200-12611400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:12611200-12612800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr7:12611200-12613200	Enhancers	Adipose Nuclei	Adipose

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