Variant report

Variant	rs4589164
Chromosome Location	chr1:169256501-169256502
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 135 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1011638	0.82[CEU][hapmap]
rs10442644	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10800418	0.86[CEU][hapmap];0.88[MEX][hapmap]
rs10800429	0.82[CEU][hapmap]
rs10800431	0.82[CEU][hapmap]
rs10800432	0.82[CEU][hapmap]
rs10919075	0.95[CEU][hapmap]
rs10919144	0.82[CEU][hapmap]
rs11802143	0.82[CEU][hapmap]
rs11808938	0.82[CEU][hapmap]
rs12080100	0.80[CEU][hapmap]
rs12084793	0.81[CEU][hapmap]
rs12116551	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12116683	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12117362	0.81[EUR][1000 genomes]
rs12117559	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12117884	0.88[EUR][1000 genomes]
rs12118611	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12118645	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12119479	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[LWK][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs12120007	0.95[CEU][hapmap];0.85[YRI][hapmap]
rs12120960	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12121185	0.88[EUR][1000 genomes]
rs12121891	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs12121994	0.95[CEU][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs12122348	0.81[EUR][1000 genomes]
rs12124049	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs12124064	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12124738	0.80[EUR][1000 genomes]
rs12125057	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12125501	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12129132	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12129567	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12129979	0.88[CEU][hapmap]
rs12130858	0.81[EUR][1000 genomes]
rs12140572	0.90[CEU][hapmap];0.85[YRI][hapmap]
rs12142784	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12143193	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs12143790	0.81[EUR][1000 genomes]
rs12143963	0.81[EUR][1000 genomes]
rs12144230	0.81[AMR][1000 genomes]
rs12144832	0.95[CEU][hapmap];1.00[YRI][hapmap]
rs12145146	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs12145193	0.81[EUR][1000 genomes]
rs12145226	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs12145897	0.95[CEU][hapmap]
rs12145969	0.82[CEU][hapmap]
rs12723917	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12728614	0.95[CEU][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs12731520	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12733626	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs12736817	0.81[EUR][1000 genomes]
rs12738167	0.88[EUR][1000 genomes]
rs12739337	0.87[EUR][1000 genomes]
rs12740501	0.81[EUR][1000 genomes]
rs12741323	0.95[CEU][hapmap]
rs12743588	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12744362	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12745978	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12750161	0.81[EUR][1000 genomes]
rs12751062	0.82[CEU][hapmap]
rs12751407	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12751571	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12753816	0.80[EUR][1000 genomes]
rs17345170	0.95[CEU][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap]
rs17345184	0.95[CEU][hapmap];1.00[YRI][hapmap]
rs17349222	0.85[MKK][hapmap]
rs17349271	0.95[CEU][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap]
rs17349439	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs17349467	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs17349579	0.94[CEU][hapmap]
rs17577184	0.82[CEU][hapmap]
rs1936533	0.94[CEU][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs2040446	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes]
rs2157597	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[EUR][1000 genomes]
rs2179491	0.95[CEU][hapmap]
rs2420010	0.81[CEU][hapmap]
rs2420014	0.87[EUR][1000 genomes]
rs2420016	0.88[EUR][1000 genomes]
rs34176173	0.80[EUR][1000 genomes]
rs34248820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34408435	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35091267	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35220898	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35249110	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35271076	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35375125	0.87[EUR][1000 genomes]
rs35393101	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35447001	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35458577	0.80[EUR][1000 genomes]
rs35539429	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36154866	0.87[EUR][1000 genomes]
rs3766077	0.81[CEU][hapmap];0.88[MEX][hapmap]
rs3766090	0.95[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs4656180	0.90[CEU][hapmap]
rs4656181	0.82[CEU][hapmap]
rs4656658	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs4656664	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs4656669	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4656671	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs4656680	0.82[CEU][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];0.85[YRI][hapmap]
rs61806242	0.81[EUR][1000 genomes]
rs61806244	0.81[EUR][1000 genomes]
rs61806989	0.82[AFR][1000 genomes]
rs61808870	0.82[EUR][1000 genomes]
rs61808916	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61808940	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6427180	0.81[CEU][hapmap]
rs6427193	0.82[ASW][hapmap]
rs6656463	0.82[ASW][hapmap]
rs6688038	0.82[CEU][hapmap]
rs6688139	0.82[CEU][hapmap]
rs6692649	0.82[YRI][hapmap]
rs71635617	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72700059	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7413522	0.82[CEU][hapmap]
rs7516097	0.81[CEU][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs7522781	0.90[EUR][1000 genomes]
rs7522896	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs7527703	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[LWK][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs7542751	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
11	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
12	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
13	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
14	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4589164	NME7	cis	Esophagus Muscularis	GTEx
rs4589164	NME7	cis	Artery Tibial	GTEx
rs4589164	NME7	cis	Thyroid	GTEx
rs4589164	NME7	cis	multi-tissue	Pritchard
rs4589164	NME7	cis	cerebellum	SCAN
rs4589164	ALDH9A1	cis	cerebellum	SCAN

Chromatin state (count:37 , 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	chr1:169251400-169271400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:169252000-169257200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:169252800-169278600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:169252800-169278800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:169253000-169264800	Weak transcription	Primary T cells from cord blood	blood
8	chr1:169253400-169270800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:169253600-169257400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:169253600-169280600	Weak transcription	Fetal Kidney	kidney
11	chr1:169253800-169258200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:169254000-169274800	Weak transcription	Ovary	ovary
13	chr1:169254400-169263600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr1:169254800-169256600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:169254800-169268600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:169254800-169281000	Weak transcription	Dnd41	blood
17	chr1:169255800-169264800	Weak transcription	Aorta	Aorta
18	chr1:169256200-169256800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr1:169256200-169256800	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr1:169256200-169257800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:169256200-169257800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:169256200-169258000	Enhancers	HSMM	muscle
23	chr1:169256200-169258600	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr1:169256200-169258800	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr1:169256200-169259200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr1:169256400-169256800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:169256400-169257000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:169256400-169257200	Enhancers	A549	lung
29	chr1:169256400-169257600	Enhancers	NH-A	brain
30	chr1:169256400-169257800	Enhancers	Muscle Satellite Cultured Cells	--
31	chr1:169256400-169257800	Enhancers	HSMMtube	muscle
32	chr1:169256400-169257800	Enhancers	HUVEC	blood vessel
33	chr1:169256400-169257800	Enhancers	Osteobl	bone
34	chr1:169256400-169258800	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr1:169256400-169258800	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr1:169256400-169258800	Enhancers	HMEC	breast
37	chr1:169256400-169258800	Enhancers	NHEK	skin

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