Variant report

Variant	rs12079062
Chromosome Location	chr1:174079584-174079585
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10158289	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10798301	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10798302	0.83[CHB][hapmap]
rs10912734	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12066153	0.83[CHB][hapmap]
rs12079063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079820	0.88[CEU][hapmap]
rs12085290	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12087441	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12094341	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12563301	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12691474	0.86[CEU][hapmap]
rs16846683	0.83[CHB][hapmap]
rs1951627	0.83[CHB][hapmap]
rs2064149	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2143114	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2294492	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2860847	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2901785	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4442420	0.88[CEU][hapmap]
rs4650945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4650989	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs4650990	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs4652169	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4652234	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4652237	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4652274	0.88[CEU][hapmap]
rs4652294	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs57919173	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60354115	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6425274	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6425275	0.83[CHB][hapmap]
rs6656188	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6658543	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6665484	0.83[CHB][hapmap]
rs6667267	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6670617	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6672986	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6677660	0.83[CHB][hapmap]
rs6681390	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6681618	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs6686083	0.83[CHB][hapmap]
rs6689285	0.83[CHB][hapmap]
rs6695327	0.83[CHB][hapmap]
rs6696076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6696163	0.83[CHB][hapmap]
rs6699146	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs714624	0.83[CHB][hapmap]
rs7413166	0.82[CHB][hapmap]
rs7526024	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7533430	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7537517	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7553788	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7555067	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs941989	0.95[CHB][hapmap]
rs972361	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916960	chr1:173907804-174080248	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	nsv465661	chr1:174014507-174152688	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv548193	chr1:174014507-174152688	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12079062	RC3H1	Cis_1M	lymphoblastoid	RTeQTL
rs12079062	RC3H1	cis	normal skin	skin_eQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174078200-174079600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:174078800-174079600	Enhancers	Primary B cells from peripheral blood	blood
3	chr1:174079000-174079800	Enhancers	GM12878-XiMat	blood
4	chr1:174079400-174079800	Enhancers	Primary B cells from cord blood	blood

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