Variant report

Variant	rs4441109
Chromosome Location	chr12:25296853-25296854
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:25293184..25295651-chr12:25296801..25299581,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10743538	0.83[ASN][1000 genomes]
rs10743543	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs10771172	0.93[AFR][1000 genomes]
rs10842474	0.81[YRI][hapmap]
rs10842479	0.93[AFR][1000 genomes]
rs10842480	0.93[AFR][1000 genomes]
rs10842481	0.93[AFR][1000 genomes]
rs10842482	0.93[AFR][1000 genomes]
rs10842484	0.93[AFR][1000 genomes]
rs10842485	0.81[ASW][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs10842486	0.87[AFR][1000 genomes]
rs11047826	0.93[CHB][hapmap]
rs11047837	0.87[ASN][1000 genomes]
rs11047842	0.89[ASN][1000 genomes]
rs11047845	0.89[ASN][1000 genomes]
rs11047853	0.93[AFR][1000 genomes]
rs11047857	0.93[ASN][1000 genomes]
rs11047863	0.88[ASW][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs11047864	0.88[ASW][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs11047880	1.00[JPT][hapmap]
rs11047882	0.85[CHD][hapmap]
rs11531007	0.93[ASN][1000 genomes]
rs11533487	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12229161	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs12229450	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12423047	0.93[ASN][1000 genomes]
rs12423778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12426684	0.90[ASN][1000 genomes]
rs12427119	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17387444	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2200402	0.88[ASW][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2220193	0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs2220195	0.88[ASW][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2291364	0.90[ASN][1000 genomes]
rs3782188	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs3924649	0.81[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes]
rs4246226	0.88[ASW][hapmap];0.97[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4280085	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs4291763	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs4418900	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs4427639	0.93[AFR][1000 genomes]
rs4460902	0.93[AFR][1000 genomes]
rs4963852	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4963853	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4963854	0.81[YRI][hapmap];0.83[AFR][1000 genomes]
rs56024196	0.81[ASN][1000 genomes]
rs7132146	0.83[ASW][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7133919	0.87[AFR][1000 genomes]
rs7298884	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs7299464	0.91[AFR][1000 genomes]
rs73069103	0.93[ASN][1000 genomes]
rs73069105	0.93[ASN][1000 genomes]
rs73077316	0.87[ASN][1000 genomes]
rs73077322	0.87[ASN][1000 genomes]
rs73079611	0.81[ASN][1000 genomes]
rs73079683	0.81[ASN][1000 genomes]
rs73081704	0.83[ASN][1000 genomes]
rs7488357	0.93[AFR][1000 genomes]
rs7959689	0.83[AFR][1000 genomes]
rs7966074	0.89[AFR][1000 genomes]
rs7966158	0.93[AFR][1000 genomes]
rs7969931	0.93[CHB][hapmap];0.95[CHD][hapmap];0.86[ASN][1000 genomes]
rs7973851	0.85[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	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription 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	22 gene(s)	inside rSNPs	diseases
5	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1041218	chr12:24972019-25304356	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv557796	chr12:25266203-25306458	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv515612	chr12:25272027-25341177	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv557797	chr12:25272027-25341177	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv898922	chr12:25274593-25408047	Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4441109	LYRM5	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25286800-25304200	Weak transcription	Ovary	ovary
2	chr12:25288800-25297400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:25293800-25303000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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