Variant report

Variant	rs7961005
Chromosome Location	chr12:75849475-75849476
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10506667	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10506669	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11180480	1.00[CEU][hapmap];0.83[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11180499	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11180552	0.83[ASN][1000 genomes]
rs11180560	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11355	0.83[ASN][1000 genomes]
rs1147995	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11540407	0.86[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs11609405	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11609538	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11610328	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11610755	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11611121	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11611609	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11612665	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11614719	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11616068	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11829445	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11829975	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12423320	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12423560	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12423750	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12424057	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12424262	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12424458	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12424779	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12425122	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12580524	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12810889	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12811343	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12812559	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12813336	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12814435	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12815116	0.83[ASN][1000 genomes]
rs12817746	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12818326	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12819511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12821144	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12822366	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822493	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs12822505	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822654	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12826635	0.83[ASN][1000 genomes]
rs12827668	0.83[ASN][1000 genomes]
rs12833944	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1501634	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs15513	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1552039	0.92[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs1604381	0.83[ASN][1000 genomes]
rs17217158	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17218895	0.83[ASN][1000 genomes]
rs17818307	0.83[ASN][1000 genomes]
rs1909977	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2054517	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2070162	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2134140	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2202105	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279244	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2306391	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs34120363	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34508642	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34522427	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34722118	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34904271	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35124104	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35244242	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35351465	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35505142	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35575314	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35619460	0.83[ASN][1000 genomes]
rs35773117	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35968211	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35986906	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36113316	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3741495	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3809118	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3809121	0.83[ASN][1000 genomes]
rs4019356	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4420306	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760596	1.00[ASN][1000 genomes]
rs4882626	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55742134	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55783970	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61932178	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61932179	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61932180	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61932209	0.80[EUR][1000 genomes]
rs61932935	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61933361	0.80[ASN][1000 genomes]
rs61933362	0.83[ASN][1000 genomes]
rs66864793	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7489329	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492067	chr12:75415458-76077537	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv899313	chr12:75715330-76057811	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv428592	chr12:75766619-75936721	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7961005	GLIPR1	cis	parietal	SCAN
rs7961005	GLIPR1L2	cis	cerebellum	SCAN
rs7961005	PTPRB	cis	parietal	SCAN
rs7961005	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75847000-75851200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:75847800-75854200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:75848600-75850600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr12:75848600-75852000	Enhancers	Dnd41	blood
5	chr12:75848800-75851800	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr12:75849000-75851600	Enhancers	Primary hematopoietic stem cells	blood
7	chr12:75849200-75850000	Enhancers	Placenta	Placenta
8	chr12:75849400-75850000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:75849400-75850000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr12:75849400-75850400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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