Variant report

Variant	rs12249377
Chromosome Location	chr10:92592956-92592957
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10881829	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10881831	0.96[ASN][1000 genomes]
rs10881833	1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs10881834	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10881835	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10881841	0.89[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10881843	0.92[ASN][1000 genomes]
rs10881845	0.89[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10881846	0.84[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs10881848	0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs10881850	0.92[CHB][hapmap];0.96[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs11186282	0.86[ASN][1000 genomes]
rs11186292	0.90[ASN][1000 genomes]
rs11186298	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11186299	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11186305	0.96[ASN][1000 genomes]
rs11186306	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11186315	0.95[ASN][1000 genomes]
rs11186323	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11186333	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs11186336	0.93[ASN][1000 genomes]
rs11186338	0.89[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11186339	0.85[ASN][1000 genomes]
rs11186343	0.92[CHB][hapmap];0.96[CHD][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs11186344	0.95[ASN][1000 genomes]
rs11186346	0.92[CHB][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs11186352	0.89[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11186358	0.90[ASN][1000 genomes]
rs11186359	0.92[CHB][hapmap];0.96[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs11186360	0.89[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11186361	0.90[ASN][1000 genomes]
rs11186367	0.92[CHB][hapmap];0.96[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs11186368	0.93[ASN][1000 genomes]
rs11498506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11498507	0.98[ASN][1000 genomes]
rs11498662	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11527868	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12220866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12244538	0.96[ASN][1000 genomes]
rs12255018	0.92[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs12256605	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12258938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12261011	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12264160	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1573253	0.90[ASN][1000 genomes]
rs1592143	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17102362	0.90[ASN][1000 genomes]
rs1891311	0.92[CHB][hapmap];0.96[CHD][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs1891312	0.92[ASN][1000 genomes]
rs2901026	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2901127	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3824739	0.81[CHD][hapmap]
rs4144422	0.92[CHB][hapmap];0.96[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs4282910	0.89[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4284320	0.90[ASN][1000 genomes]
rs4586057	0.92[CHB][hapmap];0.96[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs58578719	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59257274	0.86[ASN][1000 genomes]
rs61481895	0.92[ASN][1000 genomes]
rs7082814	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7085559	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7096568	0.92[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs73315609	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73315628	0.98[ASN][1000 genomes]
rs74148885	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7478556	0.86[ASN][1000 genomes]
rs7903584	0.90[ASN][1000 genomes]
rs7916720	0.92[CHB][hapmap];0.84[JPT][hapmap]

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	nsv467433	chr10:92083015-92598458	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv551880	chr10:92083015-92598458	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv516743	chr10:92083015-92605119	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1049931	chr10:92083932-92605364	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv948363	chr10:92084520-92614402	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv551882	chr10:92090785-92598823	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv533133	chr10:92363552-92594891	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1036058	chr10:92471568-92605364	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv831945	chr10:92590576-92793582	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
White matter microstructure (global fractional anisotropy)	24736177	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12249377	IFIT1	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:92584200-92602400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr10:92592200-92593000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
3	chr10:92592400-92593200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr10:92592600-92593000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr10:92592600-92595800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr10:92592600-92596000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr10:92592600-92596000	Enhancers	HMEC	breast
8	chr10:92592800-92593600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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