Variant report

Variant	rs10916178
Chromosome Location	chr1:227817593-227817594
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10047205	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1021553	0.82[JPT][hapmap]
rs1021554	0.81[JPT][hapmap]
rs10799432	0.87[JPT][hapmap]
rs10799435	0.87[JPT][hapmap]
rs10916165	0.87[JPT][hapmap]
rs10916182	0.86[JPT][hapmap]
rs10916187	0.83[JPT][hapmap]
rs10916192	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12025815	0.86[JPT][hapmap]
rs12059899	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12069550	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12070002	0.86[JPT][hapmap]
rs12070036	0.86[JPT][hapmap]
rs12070539	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12080321	0.87[JPT][hapmap]
rs12080590	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12082414	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12092295	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12095502	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12096675	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12132444	0.86[JPT][hapmap]
rs1495846	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1495849	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16847966	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16847991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16847992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16848029	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1923821	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2012432	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2093609	0.87[JPT][hapmap]
rs2132366	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2132367	0.86[JPT][hapmap]
rs2256599	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2453682	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2644143	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2644144	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2644146	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2644153	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2644161	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2814059	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2814060	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2814061	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2814084	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2814085	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2819496	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2819498	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2819507	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2819511	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2935146	0.87[JPT][hapmap]
rs2935152	0.86[JPT][hapmap]
rs2935155	0.86[JPT][hapmap]
rs2999745	0.87[JPT][hapmap]
rs2999746	0.87[JPT][hapmap]
rs3010183	0.86[JPT][hapmap]
rs3010186	0.86[JPT][hapmap]
rs3010190	0.87[JPT][hapmap]
rs3010191	0.86[JPT][hapmap]
rs3010192	0.86[JPT][hapmap]
rs3010193	0.86[JPT][hapmap]
rs3010194	0.87[JPT][hapmap]
rs3748806	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4376731	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4589104	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653514	0.86[JPT][hapmap]
rs4653849	0.81[JPT][hapmap]
rs4653853	0.83[JPT][hapmap]
rs58020705	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59034043	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59149651	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59753688	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61343450	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66471275	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66491073	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6659745	0.85[EUR][1000 genomes]
rs66736638	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6683151	0.86[JPT][hapmap]
rs6688145	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6693348	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66938123	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6697867	0.82[JPT][hapmap]
rs67216605	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67511833	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67676707	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68046179	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68186506	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72632830	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72632831	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72632832	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72748074	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7413796	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7528094	0.81[JPT][hapmap]
rs753541	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7539151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs903690	0.81[JPT][hapmap]
rs903692	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs903693	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs903694	1.00[CEU][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs903695	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs965942	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv945673	chr1:227799341-227819395	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10916178	C1orf142	Cis_1M	lymphoblastoid	RTeQTL
rs10916178	ZNF678	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227770000-227853800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:227790400-227834800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:227800200-227820600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:227801200-227821800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:227805800-227823600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:227811800-227830600	ZNF genes & repeats	Liver	Liver
7	chr1:227815200-227819200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:227815200-227828800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:227815400-227820800	Weak transcription	Ovary	ovary
10	chr1:227815800-227818600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:227817400-227818800	Weak transcription	Primary B cells from cord blood	blood
12	chr1:227817400-227821200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon

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