Variant report

Variant	rs2901029
Chromosome Location	chr1:169100169-169100170
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:169098857..169100595-chr1:169101188..169104374,3	MCF-7	breast:
2	chr1:169092445..169095068-chr1:169098832..169100908,2	K562	blood:
3	chr1:169074913..169078230-chr1:169098350..169100536,3	MCF-7	breast:
4	chr1:169073905..169078334-chr1:169089982..169100946,16	MCF-7	breast:
5	chr1:169098028..169100792-chr1:169101427..169102956,2	K562	blood:
6	chr1:169099064..169101885-chr1:169111160..169113548,2	K562	blood:
7	chr1:169099109..169101213-chr1:169102148..169104233,2	MCF-7	breast:
8	chr1:169092696..169095785-chr1:169096212..169101951,6	MCF-7	breast:
9	chr1:169094197..169097461-chr1:169097543..169100801,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10081959	1.00[CHB][hapmap];0.93[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10800406	0.85[AFR][1000 genomes]
rs10800407	0.82[CHB][hapmap]
rs10919064	0.89[CEU][hapmap];0.80[AMR][1000 genomes]
rs10919065	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10919066	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919073	0.82[CHB][hapmap]
rs11809180	0.82[CHB][hapmap]
rs1200154	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1200157	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1200159	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200160	0.81[CEU][hapmap]
rs12023291	0.97[CHD][hapmap];0.84[ASN][1000 genomes]
rs12070626	1.00[CHB][hapmap]
rs12079745	0.82[CHB][hapmap]
rs12082618	0.82[CHB][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes]
rs12082810	0.85[AFR][1000 genomes]
rs12083075	1.00[CHB][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12084964	0.82[CHB][hapmap]
rs12086983	0.82[CHB][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs12095171	0.82[CHB][hapmap]
rs12128543	0.92[CEU][hapmap]
rs12129969	0.88[CHB][hapmap]
rs12135928	0.85[AFR][1000 genomes]
rs12143131	0.85[AFR][1000 genomes]
rs12145939	0.82[CHB][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs12354315	0.81[ASW][hapmap];0.82[CHB][hapmap];0.84[LWK][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs12691502	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.83[ASN][1000 genomes]
rs12724494	1.00[CHB][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12728466	0.81[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12745732	0.85[AFR][1000 genomes]
rs12758208	0.82[CHB][hapmap];0.84[LWK][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs1320965	0.82[CHB][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs1320966	0.82[CHB][hapmap]
rs1320967	0.82[CHB][hapmap]
rs1358712	0.82[CHB][hapmap]
rs1419322	1.00[CHB][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1419323	0.81[ASW][hapmap];0.82[CHB][hapmap];0.81[LWK][hapmap];0.91[MKK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs1419324	0.85[AFR][1000 genomes]
rs1892094	0.82[CEU][hapmap]
rs2143287	0.82[CHB][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs2420009	0.92[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3753292	0.85[CEU][hapmap];0.91[MEX][hapmap]
rs3753293	0.93[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3766039	0.85[CEU][hapmap];0.91[MEX][hapmap]
rs3766042	0.85[CEU][hapmap]
rs3766044	0.85[CEU][hapmap]
rs3766053	0.81[ASW][hapmap];0.82[CHB][hapmap];0.84[LWK][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs3766054	0.85[AFR][1000 genomes]
rs3766055	0.82[CHB][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs3766058	0.84[ASN][1000 genomes]
rs4656177	1.00[CHB][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4656179	0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4656651	0.88[CHB][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4656652	0.93[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4656653	0.85[AFR][1000 genomes]
rs58585501	0.84[ASN][1000 genomes]
rs6664272	0.84[ASN][1000 genomes]
rs7416619	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs745922	0.81[AFR][1000 genomes]
rs7517394	0.85[CEU][hapmap]
rs7540067	0.83[CEU][hapmap]
rs7552484	0.82[CHB][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs9633334	0.96[CHD][hapmap]
rs968304	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9804101	0.84[ASN][1000 genomes]
rs9887857	0.82[CHB][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs9887903	0.85[AFR][1000 genomes]
rs9988604	0.97[CHD][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2901029	NME7	cis	Artery Tibial	GTEx
rs2901029	NME7	cis	Thyroid	GTEx
rs2901029	ALDH9A1	cis	cerebellum	SCAN
rs2901029	SELL	cis	cerebellum	SCAN
rs2901029	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169079800-169105800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:169085400-169102200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:169086200-169102000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:169086200-169102000	Weak transcription	GM12878-XiMat	blood
5	chr1:169086200-169102400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr1:169086400-169100200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:169086600-169103200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:169086600-169103400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:169089600-169101600	Genic enhancers	A549	lung
10	chr1:169089600-169103400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:169090000-169103800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:169090400-169103200	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:169091000-169102200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:169091000-169102200	Strong transcription	HepG2	liver
15	chr1:169091000-169102800	Strong transcription	Hela-S3	cervix
16	chr1:169091200-169124600	Weak transcription	NHLF	lung
17	chr1:169091400-169102200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:169091400-169103200	Strong transcription	Liver	Liver
19	chr1:169091400-169103400	Strong transcription	Duodenum Mucosa	Duodenum
20	chr1:169091600-169101200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:169091600-169102000	Weak transcription	Pancreas	Pancrea
22	chr1:169091600-169110000	Weak transcription	Spleen	Spleen
23	chr1:169091600-169120400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:169091600-169120600	Weak transcription	Lung	lung
25	chr1:169091800-169104200	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr1:169091800-169137600	Weak transcription	Esophagus	oesophagus
27	chr1:169092200-169102400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:169092400-169106200	Weak transcription	Gastric	stomach
29	chr1:169092600-169103600	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr1:169093200-169100800	Strong transcription	Primary hematopoietic stem cells	blood
31	chr1:169093200-169103200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:169093400-169102000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:169093400-169102000	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:169093400-169102800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:169093600-169102200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:169093600-169102400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:169093800-169100600	Strong transcription	Fetal Intestine Large	intestine
38	chr1:169093800-169101600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:169093800-169102200	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:169093800-169102400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr1:169093800-169102600	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:169094000-169101600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:169094400-169101000	Strong transcription	Colonic Mucosa	Colon
44	chr1:169094600-169101000	Strong transcription	Fetal Lung	lung
45	chr1:169094600-169104000	Genic enhancers	Brain Hippocampus Middle	brain
46	chr1:169095000-169100200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:169095000-169100200	Weak transcription	Primary T cells from cord blood	blood
48	chr1:169095000-169112600	Weak transcription	Stomach Mucosa	stomach
49	chr1:169095600-169101200	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr1:169095800-169106200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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