Variant report

Variant	rs4656179
Chromosome Location	chr1:169113467-169113468
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	chr1:169099064..169101885-chr1:169111160..169113548,2	K562	blood:
2	chr1:169108245..169110163-chr1:169111975..169114283,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10081959	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800406	0.94[AFR][1000 genomes]
rs10919065	0.84[ASN][1000 genomes]
rs10919066	0.82[ASN][1000 genomes]
rs1200154	0.83[ASN][1000 genomes]
rs1200157	0.84[ASN][1000 genomes]
rs1200159	0.83[ASN][1000 genomes]
rs12082618	0.89[AFR][1000 genomes]
rs12082810	0.94[AFR][1000 genomes]
rs12083075	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12086983	0.93[AFR][1000 genomes]
rs12135928	0.94[AFR][1000 genomes]
rs12143131	0.94[AFR][1000 genomes]
rs12145939	0.94[AFR][1000 genomes]
rs12354315	0.94[AFR][1000 genomes]
rs12691502	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12724494	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728466	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12745732	0.94[AFR][1000 genomes]
rs12758208	0.94[AFR][1000 genomes]
rs1320965	0.94[AFR][1000 genomes]
rs1419322	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419323	0.93[AFR][1000 genomes]
rs1419324	0.94[AFR][1000 genomes]
rs2143287	0.94[AFR][1000 genomes]
rs2420009	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901029	0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3753293	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766053	0.94[AFR][1000 genomes]
rs3766054	0.94[AFR][1000 genomes]
rs3766055	0.94[AFR][1000 genomes]
rs4656177	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656651	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656652	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656653	0.94[AFR][1000 genomes]
rs7416619	0.86[AFR][1000 genomes]
rs745922	0.89[AFR][1000 genomes]
rs7552484	0.92[AFR][1000 genomes]
rs968304	0.84[ASN][1000 genomes]
rs9887857	0.94[AFR][1000 genomes]
rs9887903	0.94[AFR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4656179	NME7	cis	Heart Left Ventricle	GTEx
rs4656179	NME7	cis	Artery Tibial	GTEx
rs4656179	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169091200-169124600	Weak transcription	NHLF	lung
2	chr1:169091600-169120400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:169091600-169120600	Weak transcription	Lung	lung
4	chr1:169091800-169137600	Weak transcription	Esophagus	oesophagus
5	chr1:169096600-169137400	Weak transcription	Fetal Stomach	stomach
6	chr1:169097000-169130000	Weak transcription	Ovary	ovary
7	chr1:169100800-169115000	Weak transcription	Small Intestine	intestine
8	chr1:169100800-169116200	Weak transcription	Fetal Kidney	kidney
9	chr1:169100800-169141400	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:169101000-169113800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:169101000-169137000	Weak transcription	Primary T cells from cord blood	blood
12	chr1:169101200-169113800	Weak transcription	Brain Germinal Matrix	brain
13	chr1:169102000-169117400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:169102400-169120600	Weak transcription	Left Ventricle	heart
15	chr1:169102800-169114800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:169103200-169116000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:169103200-169116000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:169103200-169117200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:169103200-169117400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:169103400-169130200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:169103600-169114000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:169104200-169117400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:169104800-169120400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:169104800-169142800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:169105600-169113800	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:169110400-169114800	Enhancers	Fetal Intestine Large	intestine
27	chr1:169110400-169121800	Enhancers	Fetal Intestine Small	intestine
28	chr1:169110600-169114400	Enhancers	Duodenum Mucosa	Duodenum
29	chr1:169111200-169113800	Enhancers	Liver	Liver
30	chr1:169111800-169113800	Enhancers	HepG2	liver
31	chr1:169112400-169113600	Enhancers	A549	lung
32	chr1:169112600-169114200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr1:169112600-169118400	Enhancers	Stomach Mucosa	stomach
34	chr1:169112800-169114400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr1:169112800-169120600	Weak transcription	Psoas Muscle	Psoas
36	chr1:169113000-169114000	Weak transcription	Brain Angular Gyrus	brain
37	chr1:169113000-169114200	Weak transcription	K562	blood
38	chr1:169113200-169114600	Enhancers	Brain Cingulate Gyrus	brain
39	chr1:169113400-169114200	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr1:169113400-169115400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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