Variant report

Variant	rs12743588
Chromosome Location	chr1:169263658-169263659
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10442644	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12116551	0.81[EUR][1000 genomes]
rs12116683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12117362	0.81[EUR][1000 genomes]
rs12117559	0.82[EUR][1000 genomes]
rs12117884	0.88[EUR][1000 genomes]
rs12118611	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12118645	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12120960	0.82[EUR][1000 genomes]
rs12121185	0.88[EUR][1000 genomes]
rs12121994	0.88[EUR][1000 genomes]
rs12122348	0.81[EUR][1000 genomes]
rs12124064	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12124738	0.80[EUR][1000 genomes]
rs12125057	0.81[EUR][1000 genomes]
rs12125501	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12129132	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12129567	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12130858	0.81[EUR][1000 genomes]
rs12142784	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12143193	0.88[EUR][1000 genomes]
rs12143790	0.81[EUR][1000 genomes]
rs12143963	0.81[EUR][1000 genomes]
rs12145146	0.88[EUR][1000 genomes]
rs12145193	0.81[EUR][1000 genomes]
rs12145226	0.88[EUR][1000 genomes]
rs12723917	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12728614	0.80[EUR][1000 genomes]
rs12731520	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12733626	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]
rs12744362	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12745978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12750161	0.81[EUR][1000 genomes]
rs12751407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12751571	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12753816	0.80[EUR][1000 genomes]
rs17349467	0.80[EUR][1000 genomes]
rs1936533	0.81[EUR][1000 genomes]
rs2040446	0.80[EUR][1000 genomes]
rs2157597	0.81[EUR][1000 genomes]
rs2420014	0.87[EUR][1000 genomes]
rs2420016	0.88[EUR][1000 genomes]
rs34176173	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs34248820	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34408435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35091267	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35220898	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35249110	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35271076	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35375125	0.87[EUR][1000 genomes]
rs35393101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35447001	0.80[EUR][1000 genomes]
rs35458577	0.80[EUR][1000 genomes]
rs35539429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36154866	0.87[EUR][1000 genomes]
rs3766090	0.88[EUR][1000 genomes]
rs4589164	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4656669	0.82[EUR][1000 genomes]
rs61806242	0.81[EUR][1000 genomes]
rs61806244	0.81[EUR][1000 genomes]
rs61808870	0.82[EUR][1000 genomes]
rs61808916	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61808940	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71635617	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72700059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7516097	0.81[EUR][1000 genomes]
rs7522781	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12743588	NME7	cis	Esophagus Muscularis	GTEx
rs12743588	NME7	cis	Artery Tibial	GTEx
rs12743588	NME7	cis	Thyroid	GTEx
rs12743588	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169251400-169271400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:169252800-169278600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:169252800-169278800	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr1:169253000-169264800	Weak transcription	Primary T cells from cord blood	blood
5	chr1:169253400-169270800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:169253600-169280600	Weak transcription	Fetal Kidney	kidney
7	chr1:169254000-169274800	Weak transcription	Ovary	ovary
8	chr1:169254800-169268600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:169254800-169281000	Weak transcription	Dnd41	blood
10	chr1:169255800-169264800	Weak transcription	Aorta	Aorta
11	chr1:169256800-169271600	Weak transcription	Primary B cells from cord blood	blood
12	chr1:169256800-169278600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:169257600-169268600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:169257600-169284800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:169257800-169281200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr1:169258600-169271200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:169258600-169276400	Weak transcription	HSMM	muscle
18	chr1:169258800-169264000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:169258800-169264200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:169258800-169274600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:169258800-169277400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:169259200-169278600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:169259400-169274800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:169259400-169278600	Weak transcription	Adipose Nuclei	Adipose
25	chr1:169259600-169278600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:169259600-169294400	Weak transcription	Pancreas	Pancrea
27	chr1:169260400-169310400	Weak transcription	Fetal Stomach	stomach
28	chr1:169260600-169278800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:169262400-169264000	Weak transcription	Left Ventricle	heart
30	chr1:169262400-169271400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:169262800-169274600	Weak transcription	Liver	Liver
32	chr1:169262800-169278600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:169263000-169278600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:169263400-169265600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:169263400-169265800	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr1:169263400-169265800	Weak transcription	Gastric	stomach
37	chr1:169263600-169264200	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr1:169263600-169265600	Enhancers	Primary hematopoietic stem cells	blood
39	chr1:169263600-169267600	Weak transcription	Fetal Brain Male	brain

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