Variant report

Variant	rs12664825
Chromosome Location	chr6:44252253-44252254
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:44252002..44254042-chr6:44279257..44280939,2	MCF-7	breast:
2	chr6:44250404..44254517-chr6:44264090..44267267,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146221	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10807297	0.87[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10948130	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1123523	0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12176561	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12205227	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12215176	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12943	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs170510	0.87[ASN][1000 genomes]
rs2297335	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2297336	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3187	1.00[ASW][hapmap]
rs324138	0.99[ASN][1000 genomes]
rs324139	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs324140	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs324142	1.00[ASN][1000 genomes]
rs324144	1.00[ASN][1000 genomes]
rs324145	1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs324146	1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs324147	1.00[ASN][1000 genomes]
rs325017	0.99[ASN][1000 genomes]
rs325018	0.99[ASN][1000 genomes]
rs325019	0.91[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs34865422	0.93[ASN][1000 genomes]
rs3734710	0.87[ASN][1000 genomes]
rs4714773	0.87[ASN][1000 genomes]
rs4714774	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4714776	0.81[CEU][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs516582	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs524533	0.90[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs529948	0.84[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs545970	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs551145	0.86[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs557373	1.00[ASN][1000 genomes]
rs570469	0.99[ASN][1000 genomes]
rs571770	0.91[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs614715	1.00[ASN][1000 genomes]
rs694349	0.99[ASN][1000 genomes]
rs72864308	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72864312	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72864320	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs844315	0.96[ASN][1000 genomes]
rs9349279	0.81[CEU][hapmap];0.86[MEX][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9357441	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9367190	1.00[ASW][hapmap]
rs9367191	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9369469	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9381303	1.00[ASW][hapmap]
rs9381305	0.99[ASN][1000 genomes]
rs9381306	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9381307	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9381308	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9394996	1.00[ASW][hapmap]
rs9394999	0.93[ASN][1000 genomes]
rs9395000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9395001	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[ASN][1000 genomes]
rs9395002	0.81[CEU][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS 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	201 gene(s)	inside rSNPs	diseases
2	nsv603003	chr6:44191920-44253765	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv462936	chr6:44191920-44282316	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription 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	101 gene(s)	inside rSNPs	diseases
4	nsv603004	chr6:44191920-44282316	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv885853	chr6:44197181-44274797	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv524398	chr6:44200953-44253765	Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
7	nsv885854	chr6:44211867-44274797	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
8	nsv462937	chr6:44211867-44279111	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
9	nsv603005	chr6:44211867-44279111	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12664825	C6orf138	cis	parietal	SCAN
rs12664825	HSP90AB1	cis	cerebellum	SCAN
rs12664825	ENPP5	cis	parietal	SCAN
rs12664825	PLA2G7	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44244400-44257400	Weak transcription	Pancreas	Pancrea
2	chr6:44244400-44264800	Weak transcription	Right Atrium	heart
3	chr6:44246400-44255400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:44246800-44255400	Weak transcription	Brain Germinal Matrix	brain
5	chr6:44247000-44252400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:44250000-44253800	Weak transcription	Spleen	Spleen
7	chr6:44250200-44253000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr6:44250600-44254000	Enhancers	Fetal Brain Male	brain
9	chr6:44250800-44253600	Enhancers	Fetal Brain Female	brain
10	chr6:44251000-44252600	Enhancers	Brain Angular Gyrus	brain
11	chr6:44251200-44252600	Enhancers	Brain Anterior Caudate	brain
12	chr6:44251600-44252600	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr6:44251800-44252400	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr6:44252200-44252600	Enhancers	Brain Cingulate Gyrus	brain
15	chr6:44252200-44252600	Enhancers	Brain Substantia Nigra	brain
16	chr6:44252200-44252800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:44252200-44253000	Enhancers	Brain Inferior Temporal Lobe	brain

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