Variant report

Variant	rs12699125
Chromosome Location	chr7:71654356-71654357
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10216301	1.00[JPT][hapmap]
rs10239345	0.82[ASN][1000 genomes]
rs10243592	0.82[ASN][1000 genomes]
rs10243727	0.82[ASN][1000 genomes]
rs10247132	0.82[ASN][1000 genomes]
rs10250790	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10258574	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10267684	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10274382	0.82[ASN][1000 genomes]
rs10281483	0.82[ASN][1000 genomes]
rs10950299	0.82[ASN][1000 genomes]
rs10950300	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10950302	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11981190	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1232514	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13230379	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1474389	1.00[JPT][hapmap]
rs17605262	0.82[ASN][1000 genomes]
rs17673882	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17673922	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1859485	0.83[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1996399	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2158562	1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs2428278	0.86[EUR][1000 genomes]
rs2677282	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2677284	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28447164	1.00[ASN][1000 genomes]
rs2867603	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2867605	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs34829642	0.82[ASN][1000 genomes]
rs3846985	0.83[CEU][hapmap];0.84[GIH][hapmap]
rs4577845	0.91[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4717627	1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes]
rs4717631	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4719218	0.82[ASN][1000 genomes]
rs548613	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs577091	0.83[CEU][hapmap]
rs6953054	1.00[JPT][hapmap]
rs6954622	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6957682	0.94[ASN][1000 genomes]
rs6972469	0.82[ASN][1000 genomes]
rs6974563	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6977679	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6979502	0.84[EUR][1000 genomes]
rs6979774	1.00[JPT][hapmap]
rs7786666	1.00[JPT][hapmap]
rs7787176	0.82[ASN][1000 genomes]
rs7805893	1.00[JPT][hapmap]
rs7808523	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs844719	1.00[JPT][hapmap]
rs844767	1.00[JPT][hapmap]
rs860007	1.00[JPT][hapmap]
rs860010	1.00[JPT][hapmap]
rs860013	1.00[JPT][hapmap]
rs860014	1.00[JPT][hapmap]
rs861491	0.80[AMR][1000 genomes]
rs865225	1.00[JPT][hapmap]
rs875499	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs917211	1.00[JPT][hapmap]
rs9647948	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026896	chr7:71003462-71721516	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv916220	chr7:71200006-71708048	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv531372	chr7:71300090-71909517	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv491610	chr7:71422560-71803630	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv531373	chr7:71487076-71765613	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv817506	chr7:71488542-71935721	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1034282	chr7:71531113-71876617	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv1015848	chr7:71552185-71736068	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv538942	chr7:71552185-71736068	ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv831024	chr7:71569349-71735250	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv529620	chr7:71604785-71935721	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv492243	chr7:71648955-71935721	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Lifetime average cigarettes per day in chronic obstructive pulmonary disease	21685187	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12699125	GTF2IRD1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:71641200-71686800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr7:71642400-71663000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr7:71643600-71658400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr7:71647800-71656000	Weak transcription	Thymus	Thymus
5	chr7:71649400-71656600	Weak transcription	Fetal Thymus	thymus
6	chr7:71652800-71655200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr7:71653200-71660000	Weak transcription	Primary hematopoietic stem cells	blood

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