Variant report

Variant	rs12402231
Chromosome Location	chr1:74623074-74623075
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:74623032-74623231	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:74622416..74625063-chr1:74764779..74767346,2	K562	blood:

Variant related genes	Relation type
LRRIQ3	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1032082	0.86[CHB][hapmap]
rs10493529	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs10789387	0.86[CHB][hapmap]
rs10789388	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11210404	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11210405	0.86[CHB][hapmap]
rs11210407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11210427	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs11210430	0.89[EUR][1000 genomes]
rs11210433	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11210443	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs12024616	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12026140	0.96[CEU][hapmap]
rs12029234	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.84[YRI][hapmap]
rs12029606	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12029814	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12031026	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12033705	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs12036659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs12038237	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12043976	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12046751	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12048351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12122433	0.92[JPT][hapmap]
rs12404294	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12410230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12410879	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12746942	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs12746996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12747924	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1483790	0.96[CEU][hapmap];0.99[EUR][1000 genomes]
rs1483795	0.86[CHB][hapmap]
rs17524893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17526617	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17591640	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17591703	0.90[EUR][1000 genomes]
rs17592507	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1843023	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1856789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1930588	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2035473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2128935	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs3765654	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs4142948	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4142949	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs4596834	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap]
rs4650245	0.86[CHB][hapmap]
rs6676103	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs6676622	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs6680375	0.84[ASN][1000 genomes]
rs7529384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7535929	0.86[CHB][hapmap]
rs9804006	0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9970514	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004451	chr1:74107125-74874389	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv534999	chr1:74107125-74874389	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv522147	chr1:74338530-74983835	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1003171	chr1:74407468-75122270	Strong transcription Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv535000	chr1:74407468-75122270	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1013244	chr1:74441655-74680703	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv535001	chr1:74441655-74680703	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv871269	chr1:74484753-74709362	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv871381	chr1:74484753-74712181	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers 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	8 gene(s)	inside rSNPs	diseases
10	nsv871084	chr1:74492200-74681968	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv871456	chr1:74492200-74712181	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv1008285	chr1:74517953-74705457	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
13	nsv1011308	chr1:74545016-74932777	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
14	nsv871630	chr1:74578318-74709362	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
15	nsv871909	chr1:74594901-74703758	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12402231	LRRC44	Cis_1M	lymphoblastoid	RTeQTL
rs12402231	MGC22773	cis	multi-tissue	Pritchard
rs12402231	LRRIQ3	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:74622800-74623200	Enhancers	Adipose Nuclei	Adipose

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