Variant report

Variant	rs12140572
Chromosome Location	chr1:169325127-169325128
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169324847..169326824-chr1:169332989..169335675,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1014965	0.83[EUR][1000 genomes]
rs10442644	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs12116551	0.86[CEU][hapmap];0.85[YRI][hapmap]
rs12118611	0.90[CEU][hapmap];0.85[YRI][hapmap]
rs12119479	0.82[CEU][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs12120007	0.86[CEU][hapmap]
rs12121891	0.84[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs12121994	0.85[CEU][hapmap]
rs12124049	0.83[CEU][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs12125501	0.90[CEU][hapmap]
rs12143193	0.86[CEU][hapmap]
rs12143708	0.83[AFR][1000 genomes]
rs12144832	0.86[CEU][hapmap];0.85[YRI][hapmap]
rs12145146	0.86[CEU][hapmap]
rs12145226	0.86[CEU][hapmap]
rs12728614	0.86[CEU][hapmap];0.85[YRI][hapmap]
rs12730053	0.83[AFR][1000 genomes]
rs12733626	0.86[CEU][hapmap]
rs12741323	0.86[CEU][hapmap]
rs12750775	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12758228	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17345184	0.86[CEU][hapmap];0.87[YRI][hapmap]
rs17349439	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs17349467	0.86[CEU][hapmap];0.87[YRI][hapmap]
rs17349579	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17577184	0.83[CEU][hapmap]
rs1936533	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs2040446	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs2157597	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs35010461	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs35107735	0.83[AFR][1000 genomes]
rs35220898	0.91[CEU][hapmap];0.87[YRI][hapmap]
rs3766090	0.85[CEU][hapmap]
rs4589164	0.90[CEU][hapmap];0.85[YRI][hapmap]
rs4656182	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4656658	0.85[CEU][hapmap];0.87[YRI][hapmap]
rs4656664	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs4656671	0.82[CEU][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4656674	0.84[EUR][1000 genomes]
rs4656677	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4656678	0.83[AFR][1000 genomes]
rs4656680	0.82[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs61806989	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61807017	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7368145	0.93[AFR][1000 genomes]
rs7516097	1.00[YRI][hapmap]
rs7522896	0.86[CEU][hapmap];0.83[YRI][hapmap]
rs7527703	0.82[CEU][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7542751	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
5	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
6	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
7	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv3404638	chr1:169322853-169325701	Weak transcription Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv3371577	chr1:169323203-169325576	Weak transcription Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv3404056	chr1:169323578-169325326	Weak transcription Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12140572	NME7	cis	Thyroid	GTEx
rs12140572	NME7	cis	Artery Tibial	GTEx
rs12140572	NME7	cis	Esophagus Muscularis	GTEx
rs12140572	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:169305600-169336400	Weak transcription	Left Ventricle	heart
3	chr1:169309200-169333600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:169309400-169336400	Weak transcription	Ovary	ovary
5	chr1:169310800-169332800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:169311000-169336400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:169316000-169334200	Weak transcription	Fetal Intestine Small	intestine
8	chr1:169317000-169336400	Weak transcription	Pancreas	Pancrea
9	chr1:169317200-169333800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:169317800-169332800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:169317800-169333800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:169317800-169335800	Weak transcription	Fetal Lung	lung
13	chr1:169318000-169332200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:169318200-169334000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:169324600-169335800	Weak transcription	Primary T cells from cord blood	blood
16	chr1:169324800-169325200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:169324800-169325600	Enhancers	K562	blood
18	chr1:169325000-169331800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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