Variant report

Variant	rs2420008
Chromosome Location	chr1:169110425-169110426
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	chr1:169104511..169107059-chr1:169109794..169111882,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10081960	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1018831	0.82[JPT][hapmap]
rs1040502	1.00[CHB][hapmap]
rs10732287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10800408	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs10800424	0.82[JPT][hapmap]
rs10800425	0.82[JPT][hapmap]
rs10919075	0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs10919124	0.82[JPT][hapmap]
rs1200079	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1200085	0.82[JPT][hapmap]
rs1200160	1.00[CHB][hapmap]
rs1200161	0.80[ASN][1000 genomes]
rs1200164	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs1208327	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1208370	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs12084793	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs12086665	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137282	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138150	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12691502	0.83[CEU][hapmap]
rs12724494	0.95[CEU][hapmap]
rs12728466	0.83[CEU][hapmap]
rs12731646	0.91[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12752748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419322	0.87[CEU][hapmap]
rs1591733	0.82[JPT][hapmap]
rs16861990	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17345107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17345170	0.85[TSI][hapmap]
rs17349222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17349271	0.85[TSI][hapmap]
rs1829286	0.83[ASN][1000 genomes]
rs1856303	0.82[JPT][hapmap]
rs1892094	1.00[CHB][hapmap]
rs2037250	0.82[JPT][hapmap]
rs2179490	0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179491	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs35152438	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766042	0.83[LWK][hapmap]
rs3766044	1.00[CHB][hapmap]
rs3766057	0.82[JPT][hapmap]
rs4264046	0.82[JPT][hapmap]
rs4656177	0.83[CEU][hapmap];0.81[YRI][hapmap]
rs4656178	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656180	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4656651	0.86[CEU][hapmap];0.82[YRI][hapmap]
rs61803315	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61803316	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67450288	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7520186	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7522760	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533257	0.82[JPT][hapmap]
rs7540067	1.00[CHB][hapmap]
rs7542713	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754550	1.00[CHB][hapmap]
rs754551	1.00[CHB][hapmap]
rs7552323	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2420008	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs2420008	NME7	cis	cerebellum	SCAN

Chromatin state (count:39 , 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	chr1:169095000-169112600	Weak transcription	Stomach Mucosa	stomach
6	chr1:169096600-169137400	Weak transcription	Fetal Stomach	stomach
7	chr1:169097000-169130000	Weak transcription	Ovary	ovary
8	chr1:169098800-169112200	Weak transcription	HSMM	muscle
9	chr1:169099400-169111200	Weak transcription	Aorta	Aorta
10	chr1:169099400-169112000	Weak transcription	Psoas Muscle	Psoas
11	chr1:169100800-169115000	Weak transcription	Small Intestine	intestine
12	chr1:169100800-169116200	Weak transcription	Fetal Kidney	kidney
13	chr1:169100800-169141400	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:169101000-169113800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:169101000-169137000	Weak transcription	Primary T cells from cord blood	blood
16	chr1:169101200-169113800	Weak transcription	Brain Germinal Matrix	brain
17	chr1:169102000-169117400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:169102400-169120600	Weak transcription	Left Ventricle	heart
19	chr1:169102800-169112600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:169102800-169114800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:169103200-169111200	Weak transcription	Liver	Liver
22	chr1:169103200-169116000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:169103200-169116000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:169103200-169117200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:169103200-169117400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:169103400-169110600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:169103400-169110600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:169103400-169130200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:169103600-169114000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr1:169104200-169117400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr1:169104800-169120400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:169104800-169142800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:169105600-169113800	Weak transcription	Brain Hippocampus Middle	brain
34	chr1:169109200-169110800	Enhancers	A549	lung
35	chr1:169109800-169111200	Weak transcription	HepG2	liver
36	chr1:169110400-169110600	Enhancers	Osteobl	bone
37	chr1:169110400-169111600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:169110400-169114800	Enhancers	Fetal Intestine Large	intestine
39	chr1:169110400-169121800	Enhancers	Fetal Intestine Small	intestine

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