Variant report

Variant	rs35133990
Chromosome Location	chr1:169124720-169124721
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169124501..169127273-chr1:169133900..169136216,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10919075	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12084793	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12116551	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12117362	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12117559	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12120007	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12120960	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12122348	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12124738	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12125057	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12130858	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12143790	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12143963	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12144230	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12144832	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12145193	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12145897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12728614	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12730917	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12730920	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12736817	0.91[EUR][1000 genomes]
rs12740501	0.91[EUR][1000 genomes]
rs12741323	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12750161	0.91[EUR][1000 genomes]
rs12753816	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17345170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17345184	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17349222	0.87[AFR][1000 genomes]
rs17349271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17349439	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17349467	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1936533	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2040446	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2157597	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2179491	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34829200	0.82[EUR][1000 genomes]
rs34975352	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35447001	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35458577	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4656178	0.85[AFR][1000 genomes]
rs4656180	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4656658	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4656664	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4656669	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61806190	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61806208	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61806242	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61806244	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61808870	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs745921	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7516097	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7519279	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs35133990	NME7	cis	Thyroid	GTEx
rs35133990	NME7	cis	Esophagus Muscularis	GTEx
rs35133990	NME7	cis	Artery Tibial	GTEx
rs35133990	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169091800-169137600	Weak transcription	Esophagus	oesophagus
2	chr1:169096600-169137400	Weak transcription	Fetal Stomach	stomach
3	chr1:169097000-169130000	Weak transcription	Ovary	ovary
4	chr1:169100800-169141400	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:169101000-169137000	Weak transcription	Primary T cells from cord blood	blood
6	chr1:169103400-169130200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:169104800-169142800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:169115800-169130400	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:169116200-169130200	Weak transcription	Brain Anterior Caudate	brain
10	chr1:169116400-169126600	Weak transcription	Right Atrium	heart
11	chr1:169116400-169139400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:169118000-169137000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:169118200-169130400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:169118400-169126000	Weak transcription	Stomach Mucosa	stomach
15	chr1:169118400-169126400	Weak transcription	Small Intestine	intestine
16	chr1:169118600-169130000	Weak transcription	Liver	Liver
17	chr1:169120400-169130200	Weak transcription	A549	lung
18	chr1:169120600-169125200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:169120800-169125200	Weak transcription	Right Ventricle	heart
20	chr1:169121000-169125200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:169121000-169125600	Weak transcription	Colonic Mucosa	Colon
22	chr1:169121000-169129200	Weak transcription	Lung	lung
23	chr1:169121000-169137000	Weak transcription	Psoas Muscle	Psoas
24	chr1:169121000-169140800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:169121200-169141200	Weak transcription	Left Ventricle	heart
26	chr1:169121800-169143000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:169122600-169130200	Weak transcription	NHEK	skin
28	chr1:169122800-169136400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:169124200-169127600	Enhancers	Fetal Intestine Large	intestine
30	chr1:169124400-169124800	Enhancers	Gastric	stomach
31	chr1:169124400-169125000	Enhancers	Duodenum Mucosa	Duodenum
32	chr1:169124400-169125400	Enhancers	Fetal Heart	heart
33	chr1:169124400-169125400	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr1:169124400-169128000	Enhancers	Fetal Intestine Small	intestine
35	chr1:169124600-169124800	Enhancers	NHLF	lung
36	chr1:169124600-169125400	Enhancers	Colon Smooth Muscle	Colon
37	chr1:169124600-169130200	Weak transcription	Stomach Smooth Muscle	stomach

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