Variant report

Variant	rs12129567
Chromosome Location	chr1:169283192-169283193
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	GATA3	chr1:169282971-169283507	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169281102..169283906-chr1:169293701..169295205,2	K562	blood:

Variant related genes	Relation type
NME7	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10442644	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12116683	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12117559	0.81[EUR][1000 genomes]
rs12117884	0.87[EUR][1000 genomes]
rs12118611	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12118645	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12120960	0.81[EUR][1000 genomes]
rs12121185	0.87[EUR][1000 genomes]
rs12121994	0.87[EUR][1000 genomes]
rs12124064	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12125501	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12129132	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12142784	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12143193	0.87[EUR][1000 genomes]
rs12145146	0.87[EUR][1000 genomes]
rs12145226	0.87[EUR][1000 genomes]
rs12723917	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12731520	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12733626	0.86[EUR][1000 genomes]
rs12738167	0.87[EUR][1000 genomes]
rs12739337	0.86[EUR][1000 genomes]
rs12743588	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12744362	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12745978	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12751407	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12751571	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2420014	0.86[EUR][1000 genomes]
rs2420016	0.87[EUR][1000 genomes]
rs34248820	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34408435	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35091267	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35220898	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35249110	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35271076	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35375125	0.86[EUR][1000 genomes]
rs35393101	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35539429	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs36154866	0.86[EUR][1000 genomes]
rs3766090	0.87[EUR][1000 genomes]
rs4589164	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4656669	0.81[EUR][1000 genomes]
rs61808870	0.81[EUR][1000 genomes]
rs61808916	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61808940	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71635617	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72700059	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7522781	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12129567	NME7	cis	Artery Tibial	GTEx
rs12129567	NME7	cis	Esophagus Muscularis	GTEx
rs12129567	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs12129567	NME7	cis	Thyroid	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169257600-169284800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:169259600-169294400	Weak transcription	Pancreas	Pancrea
3	chr1:169260400-169310400	Weak transcription	Fetal Stomach	stomach
4	chr1:169264400-169294400	Weak transcription	Left Ventricle	heart
5	chr1:169265000-169320400	Weak transcription	Aorta	Aorta
6	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:169271800-169297200	Weak transcription	Psoas Muscle	Psoas
8	chr1:169273600-169312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:169276800-169304600	Weak transcription	Ovary	ovary
10	chr1:169277000-169294600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:169277000-169306200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:169278000-169285800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:169279000-169288400	Weak transcription	Brain Angular Gyrus	brain
14	chr1:169279000-169291200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:169279000-169293800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:169279000-169295600	Weak transcription	Adipose Nuclei	Adipose
17	chr1:169279200-169287200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:169279200-169296000	Weak transcription	Primary T cells from cord blood	blood
19	chr1:169280200-169304600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:169281200-169283400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:169281600-169294400	Weak transcription	Fetal Intestine Small	intestine
22	chr1:169281600-169294400	Weak transcription	Lung	lung
23	chr1:169281600-169306600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:169281800-169295400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr1:169282000-169285800	Weak transcription	HUVEC	blood vessel
26	chr1:169282000-169286000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:169282000-169288800	Weak transcription	A549	lung
28	chr1:169282000-169289600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:169282000-169290600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:169282000-169293800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:169282000-169294600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:169282000-169306800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:169282200-169293600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:169282200-169295800	Weak transcription	NHEK	skin
35	chr1:169282400-169289200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:169282400-169295600	Weak transcription	NH-A	brain
37	chr1:169282800-169285800	Weak transcription	Hela-S3	cervix
38	chr1:169283000-169290400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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