Variant report

Variant	rs3106121
Chromosome Location	chr1:149778729-149778730
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1044808	1.00[CEU][hapmap]
rs1046332	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes]
rs12078573	0.81[CEU][hapmap]
rs1349532	1.00[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs1376676	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs1451641	1.00[CEU][hapmap]
rs15931	1.00[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs16835135	0.90[CEU][hapmap]
rs16836630	0.90[CEU][hapmap]
rs17643644	0.81[CEU][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap]
rs2474478	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72708145	0.86[AMR][1000 genomes]
rs7544531	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002340	chr1:148916177-149778729	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	394 gene(s)	inside rSNPs	diseases
2	nsv432820	chr1:148921404-149920927	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	784 gene(s)	inside rSNPs	diseases
3	nsv869912	chr1:148936712-149815117	Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	413 gene(s)	inside rSNPs	diseases
4	esv1809518	chr1:149004461-149787386	Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
5	esv1806395	chr1:149015282-149849940	Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	425 gene(s)	inside rSNPs	diseases
6	esv1831586	chr1:149036382-149849940	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	425 gene(s)	inside rSNPs	diseases
7	esv1827746	chr1:149038756-149797917	Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	405 gene(s)	inside rSNPs	diseases
8	nsv872384	chr1:149211496-149815536	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
9	nsv824553	chr1:149581035-149782803	Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
10	nsv824564	chr1:149581035-149815116	Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
11	esv18080	chr1:149622963-149801822	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv831503	chr1:149640643-149820841	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
13	nsv469694	chr1:149688852-149836280	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
14	nsv482790	chr1:149688852-149836280	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
15	nsv831525	chr1:149701537-149878033	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
16	esv18420	chr1:149707658-149795271	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
17	nsv946376	chr1:149729856-149783106	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3106121	LOC653604	cis	multi-tissue	Pritchard
rs3106121	LOC653610	cis	multi-tissue	Pritchard
rs3106121	HIST2H4	cis	multi-tissue	Pritchard
rs3106121	FCGR1A	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:149764800-149781400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr1:149765200-149782200	Weak transcription	Fetal Thymus	thymus
3	chr1:149765600-149779800	Weak transcription	Ovary	ovary
4	chr1:149765600-149782200	Weak transcription	Fetal Intestine Large	intestine
5	chr1:149775400-149781800	Weak transcription	Primary B cells from cord blood	blood
6	chr1:149776600-149782200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:149777600-149782600	Weak transcription	Pancreas	Pancrea
8	chr1:149778600-149778800	Flanking Active TSS	K562	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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