Variant report

Variant	rs7798693
Chromosome Location	chr7:150358296-150358297
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:150345053..150347622-chr7:150357976..150360904,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10046529	0.92[ASN][1000 genomes]
rs10236990	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10256456	0.92[ASN][1000 genomes]
rs10256482	0.92[ASN][1000 genomes]
rs10260218	0.89[AFR][1000 genomes]
rs10265794	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10266069	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10279166	0.84[ASN][1000 genomes]
rs10280903	0.86[EUR][1000 genomes]
rs10807983	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10952282	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1234365	0.88[ASN][1000 genomes]
rs12703092	0.89[AFR][1000 genomes]
rs13230712	0.92[ASN][1000 genomes]
rs1916016	0.93[ASN][1000 genomes]
rs1916017	0.93[ASN][1000 genomes]
rs1916018	0.93[ASN][1000 genomes]
rs1916019	0.93[ASN][1000 genomes]
rs1916020	0.92[ASN][1000 genomes]
rs1916021	0.92[ASN][1000 genomes]
rs1916028	0.81[JPT][hapmap]
rs2049247	0.89[AFR][1000 genomes]
rs2140143	0.92[ASN][1000 genomes]
rs2140144	0.89[AFR][1000 genomes]
rs2373843	0.92[ASN][1000 genomes]
rs28671726	0.93[ASN][1000 genomes]
rs28818858	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6952669	0.85[EUR][1000 genomes]
rs6962505	0.90[AFR][1000 genomes]
rs6965316	0.91[ASN][1000 genomes]
rs6969792	0.92[ASN][1000 genomes]
rs6970218	0.92[ASN][1000 genomes]
rs6974171	0.92[ASN][1000 genomes]
rs7776607	0.92[ASN][1000 genomes]
rs7776654	0.92[ASN][1000 genomes]
rs7776790	0.92[ASN][1000 genomes]
rs7786504	0.91[ASN][1000 genomes]
rs7795079	0.85[EUR][1000 genomes]
rs9655603	0.92[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	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	esv2758617	chr7:150251949-150463804	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2759573	chr7:150251949-150463804	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv3388935	chr7:150301204-150374532	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1030109	chr7:150312916-150701010	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv967475	chr7:150323577-150610034	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv831187	chr7:150325913-150503500	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7798693	LR8	cis	multi-tissue	Pritchard
rs7798693	HCA112	cis	multi-tissue	Pritchard
rs7798693	MLL3	cis	parietal	SCAN
rs7798693	GIMAP8	Cis_1M	lymphoblastoid	RTeQTL
rs7798693	GIMAP5	cis	lymphoblastoid	seeQTL
rs7798693	GIMAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150354800-150362000	Weak transcription	Right Atrium	heart
2	chr7:150355200-150358400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr7:150355800-150360800	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr7:150356600-150358600	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr7:150357600-150365000	Enhancers	Primary T cells from cord blood	blood
6	chr7:150358000-150360800	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr7:150358000-150360800	Enhancers	Dnd41	blood
8	chr7:150358000-150365400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr7:150358000-150369000	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr7:150358200-150358800	Flanking Active TSS	GM12878-XiMat	blood
11	chr7:150358200-150360800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr7:150358200-150360800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr7:150358200-150360800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr7:150358200-150360800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr7:150358200-150360800	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr7:150358200-150360800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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