Variant report

Variant	rs3000101
Chromosome Location	chr1:79985166-79985167
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	RUNX3	chr1:79985049-79985418	GM12878	blood:	n/a	n/a
2	ATF2	chr1:79985113-79985414	GM12878	blood:	n/a	n/a
3	RUNX3	chr1:79984917-79985493	GM12878	blood:	n/a	n/a
4	NFIC	chr1:79985018-79985562	GM12878	blood:	n/a	n/a
5	STAT5A	chr1:79985053-79985408	GM12878	blood:	n/a	n/a
6	ATF2	chr1:79985055-79985451	GM12878	blood:	n/a	n/a
7	MEF2A	chr1:79984944-79985531	GM12878	blood:	n/a	chr1:79985373-79985384 chr1:79985372-79985387 chr1:79985374-79985383 chr1:79985178-79985189 chr1:79985370-79985385 chr1:79985374-79985385 chr1:79985371-79985387 chr1:79985372-79985387 chr1:79985179-79985188
8	FOXM1	chr1:79984984-79985517	GM12878	blood:	n/a	n/a
9	NFIC	chr1:79984798-79985599	GM12878	blood:	n/a	n/a
10	CREB1	chr1:79985043-79985496	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ADH5P2	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10493629	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11588913	0.82[AMR][1000 genomes]
rs12727530	0.83[AMR][1000 genomes]
rs12727721	0.85[AMR][1000 genomes]
rs12739748	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12739762	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1353290	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1389940	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1389942	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1389943	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1389944	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1389946	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1389947	0.86[ASN][1000 genomes]
rs1494856	0.85[AMR][1000 genomes]
rs1494857	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17418579	0.84[AMR][1000 genomes]
rs17453037	0.87[AMR][1000 genomes]
rs1994938	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2029788	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2101800	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2132057	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2860503	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2934867	0.81[AMR][1000 genomes]
rs2934868	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2934871	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2934873	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2934878	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3000098	0.81[EUR][1000 genomes]
rs3000110	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3000142	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000148	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3000155	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3000174	0.81[EUR][1000 genomes]
rs3000175	0.81[EUR][1000 genomes]
rs3000176	0.81[EUR][1000 genomes]
rs3000177	0.81[EUR][1000 genomes]
rs3000179	0.81[EUR][1000 genomes]
rs3015006	0.82[EUR][1000 genomes]
rs3015008	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3015013	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3015014	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3015017	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3015019	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015021	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3015022	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015107	0.81[EUR][1000 genomes]
rs3122389	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35624469	0.87[AMR][1000 genomes]
rs35938583	0.81[AMR][1000 genomes]
rs4506421	0.80[CHB][hapmap];0.87[AMR][1000 genomes]
rs58635031	0.81[AMR][1000 genomes]
rs59395170	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004014	chr1:79811049-80042309	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1012004	chr1:79945395-80096748	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv535017	chr1:79945395-80096748	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1012296	chr1:79945395-80300216	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1005022	chr1:79950774-80106902	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv546636	chr1:79964823-80079996	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv546637	chr1:79984748-80159969	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79983000-79985200	Enhancers	Primary T cells from cord blood	blood
2	chr1:79984400-79985400	Enhancers	GM12878-XiMat	blood

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