Variant report

Variant	rs12092528
Chromosome Location	chr1:169253984-169253985
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 118 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10800410	0.81[AMR][1000 genomes]
rs10800411	0.81[AMR][1000 genomes]
rs10800415	0.86[AMR][1000 genomes]
rs10800417	0.86[AMR][1000 genomes]
rs10800419	0.85[AMR][1000 genomes]
rs10800420	0.86[AMR][1000 genomes]
rs10919084	0.81[AMR][1000 genomes]
rs10919090	0.81[AMR][1000 genomes]
rs10919094	0.81[AMR][1000 genomes]
rs10919106	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10919107	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10919108	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11802117	0.81[AMR][1000 genomes]
rs11802143	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11808938	0.86[AMR][1000 genomes]
rs11809256	0.86[AMR][1000 genomes]
rs12059281	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12065884	0.81[AMR][1000 genomes]
rs12067018	0.80[AMR][1000 genomes]
rs12067072	0.80[AMR][1000 genomes]
rs12071277	0.81[AMR][1000 genomes]
rs12075832	0.81[AMR][1000 genomes]
rs12081283	0.86[AMR][1000 genomes]
rs12083287	0.80[AMR][1000 genomes]
rs12084549	0.86[AMR][1000 genomes]
rs12084957	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12085114	0.81[EUR][1000 genomes]
rs12120493	0.81[AMR][1000 genomes]
rs12121346	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12121395	0.85[AMR][1000 genomes]
rs12123168	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12125921	0.81[AMR][1000 genomes]
rs12125985	0.81[AMR][1000 genomes]
rs12126032	0.81[AMR][1000 genomes]
rs12126266	0.86[AMR][1000 genomes]
rs12127305	0.81[AMR][1000 genomes]
rs12130764	0.81[AMR][1000 genomes]
rs12141151	0.86[AMR][1000 genomes]
rs12141917	0.86[AMR][1000 genomes]
rs12145969	0.86[AMR][1000 genomes]
rs12568636	0.81[AMR][1000 genomes]
rs12724093	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12724863	0.81[AMR][1000 genomes]
rs12734206	0.81[AMR][1000 genomes]
rs12736723	0.81[AMR][1000 genomes]
rs12739920	0.86[AMR][1000 genomes]
rs12740040	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12741540	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12745997	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12747242	0.80[AMR][1000 genomes]
rs12751062	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12756799	0.81[AMR][1000 genomes]
rs1830493	0.80[AMR][1000 genomes]
rs1830495	0.81[AMR][1000 genomes]
rs2012763	0.88[AMR][1000 genomes]
rs2032044	0.81[AMR][1000 genomes]
rs2050119	0.80[AMR][1000 genomes]
rs2300159	0.85[AMR][1000 genomes]
rs2420012	0.86[AMR][1000 genomes]
rs34250651	0.81[AMR][1000 genomes]
rs35631014	0.81[AMR][1000 genomes]
rs35774511	0.81[AMR][1000 genomes]
rs36079696	0.86[AMR][1000 genomes]
rs3753297	0.86[AMR][1000 genomes]
rs3753300	0.86[AMR][1000 genomes]
rs3766059	0.81[AMR][1000 genomes]
rs3766060	0.81[AMR][1000 genomes]
rs3766061	0.81[AMR][1000 genomes]
rs3766062	0.81[AMR][1000 genomes]
rs3766065	0.80[AMR][1000 genomes]
rs3766067	0.81[AMR][1000 genomes]
rs3766069	0.81[AMR][1000 genomes]
rs3766070	0.81[AMR][1000 genomes]
rs3766071	0.81[AMR][1000 genomes]
rs3820056	0.81[AMR][1000 genomes]
rs4385775	0.86[AMR][1000 genomes]
rs4445529	0.86[AMR][1000 genomes]
rs4656181	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4656659	0.81[AMR][1000 genomes]
rs4656660	0.84[AMR][1000 genomes]
rs4656662	0.86[AMR][1000 genomes]
rs4656666	0.86[AMR][1000 genomes]
rs4656667	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61806209	0.81[AMR][1000 genomes]
rs6679084	0.86[AMR][1000 genomes]
rs6688038	0.84[AMR][1000 genomes]
rs6688139	0.86[AMR][1000 genomes]
rs6695177	0.81[AMR][1000 genomes]
rs6695252	0.81[AMR][1000 genomes]
rs6703463	0.86[AMR][1000 genomes]
rs6704482	0.86[AMR][1000 genomes]
rs72700019	0.86[AMR][1000 genomes]
rs7518554	0.81[AMR][1000 genomes]
rs7541675	0.81[AMR][1000 genomes]
rs7547686	0.80[AMR][1000 genomes]
rs909929	0.81[AMR][1000 genomes]
rs909930	0.81[AMR][1000 genomes]
rs909931	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv429913	chr1:169177019-169296744	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1012919	chr1:169200982-169324750	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1000254	chr1:169203554-169271792	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1009170	chr1:169207940-169270995	Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv1804244	chr1:169213979-169255892	Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv508637	chr1:169214920-169268078	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv820717	chr1:169220418-169254128	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv825376	chr1:169220418-169254683	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv1815560	chr1:169226902-169256501	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
15	esv1815844	chr1:169226902-169256501	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv825398	chr1:169226944-169254128	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv870186	chr1:169227203-169254119	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv548163	chr1:169229144-169256501	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv1004674	chr1:169233962-169271792	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	esv2761410	chr1:169233974-169255402	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12092528	NME7	cis	Esophagus Muscularis	GTEx
rs12092528	NME7	cis	Thyroid	GTEx
rs12092528	NME7	cis	Artery Tibial	GTEx
rs12092528	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169227600-169257400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:169228400-169257400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:169249200-169255800	Weak transcription	Fetal Heart	heart
4	chr1:169251400-169271400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:169252000-169257200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:169252600-169256200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:169252600-169256400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:169252800-169278600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:169252800-169278800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:169253000-169254600	Weak transcription	HSMM	muscle
11	chr1:169253000-169264800	Weak transcription	Primary T cells from cord blood	blood
12	chr1:169253200-169255000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:169253400-169256400	Weak transcription	HUVEC	blood vessel
14	chr1:169253400-169270800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:169253600-169254000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr1:169253600-169256400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:169253600-169256400	Weak transcription	NH-A	brain
18	chr1:169253600-169257400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:169253600-169280600	Weak transcription	Fetal Kidney	kidney
20	chr1:169253800-169256200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:169253800-169256200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:169253800-169258200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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