Variant report

Variant	rs12192817
Chromosome Location	chr6:45534381-45534382
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	chr6:45533105..45535281-chr6:45537536..45540429,2	MCF-7	breast:
2	chr6:45533723..45535563-chr6:45552658..45554257,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SUPT3H-1	chr6:45534240-45535428	NONHSAT112988

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1041334	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12201995	0.99[EUR][1000 genomes]
rs12202314	0.89[ASN][1000 genomes]
rs12664797	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13200687	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs13205082	0.80[EUR][1000 genomes]
rs16873510	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1928529	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1928530	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1928531	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1928532	0.89[ASN][1000 genomes]
rs35611098	0.99[EUR][1000 genomes]
rs3763191	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs68057028	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6938214	0.87[EUR][1000 genomes]
rs6938450	1.00[CHB][hapmap]
rs7752324	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7758107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7758317	0.81[ASN][1000 genomes]
rs9463100	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][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	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv427755	chr6:45474631-45627025	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1019561	chr6:45485826-45535222	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv538214	chr6:45485826-45535222	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv603009	chr6:45530471-45543530	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv462940	chr6:45532214-45545975	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv603010	chr6:45532214-45545975	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12192817	YIPF3	cis	parietal	SCAN
rs12192817	C6orf138	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45522000-45536800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:45524800-45537000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:45525000-45534600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:45531000-45536200	Weak transcription	Psoas Muscle	Psoas
5	chr6:45531000-45537000	Weak transcription	Ovary	ovary
6	chr6:45531000-45537200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:45532400-45537000	Weak transcription	Fetal Heart	heart
8	chr6:45532600-45536200	Weak transcription	Left Ventricle	heart
9	chr6:45532800-45535600	Weak transcription	Right Atrium	heart
10	chr6:45533800-45535000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:45533800-45535400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr6:45533800-45537400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:45534000-45534400	Weak transcription	HSMM	muscle
14	chr6:45534000-45537600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr6:45534200-45534400	Enhancers	HSMMtube	muscle
16	chr6:45534200-45534800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:45534200-45535400	Enhancers	HepG2	liver
18	chr6:45534200-45535400	Enhancers	NH-A	brain
19	chr6:45534200-45537800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:45534200-45538000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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