Variant report

Variant	rs12691502
Chromosome Location	chr1:169112631-169112632
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: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10081959	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800407	0.82[CHB][hapmap]
rs10919065	1.00[CHB][hapmap];0.81[GIH][hapmap];0.84[ASN][1000 genomes]
rs10919066	0.82[ASN][1000 genomes]
rs10919073	0.82[CHB][hapmap]
rs10919086	0.86[CHD][hapmap]
rs11809180	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs1200154	0.83[ASN][1000 genomes]
rs1200157	0.84[ASN][1000 genomes]
rs1200159	0.83[ASN][1000 genomes]
rs12023291	0.84[CHD][hapmap]
rs12067018	0.86[CHD][hapmap]
rs12070626	1.00[CHB][hapmap]
rs12072226	0.85[CHD][hapmap]
rs12079745	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12082618	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs12083075	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12084964	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs12086665	0.83[CEU][hapmap]
rs12086983	0.82[CHB][hapmap]
rs12095171	0.82[CHB][hapmap]
rs12124168	0.85[CHD][hapmap]
rs12129969	0.88[CHB][hapmap]
rs12137282	0.90[CEU][hapmap]
rs12145939	0.82[CHB][hapmap]
rs12354315	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[TSI][hapmap]
rs12562404	0.86[CHD][hapmap]
rs12724494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728466	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];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12744184	0.86[CHD][hapmap]
rs12752748	0.83[CEU][hapmap]
rs12755385	0.86[CHD][hapmap]
rs12758208	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs1320965	0.82[CHB][hapmap]
rs1320966	0.82[CHB][hapmap]
rs1320967	0.82[CHB][hapmap]
rs1358712	0.82[CHB][hapmap]
rs1419322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419323	0.82[CHB][hapmap];0.81[CHD][hapmap];0.84[TSI][hapmap]
rs17345107	0.83[CEU][hapmap]
rs17349222	0.83[CEU][hapmap]
rs2143287	0.82[CHB][hapmap]
rs2420008	0.83[CEU][hapmap]
rs2420009	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901029	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.83[ASN][1000 genomes]
rs3737681	0.86[CHD][hapmap]
rs3753293	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766053	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[TSI][hapmap]
rs3766055	0.82[CHB][hapmap]
rs3766060	0.86[CHD][hapmap]
rs3820055	0.86[CHD][hapmap]
rs3820056	0.86[CHD][hapmap]
rs4656177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656179	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656651	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656652	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541564	0.86[CHD][hapmap]
rs7541675	0.86[CHD][hapmap]
rs7552323	0.83[CEU][hapmap]
rs7552484	0.82[CHB][hapmap]
rs909930	0.86[CHD][hapmap]
rs909931	0.86[CHD][hapmap]
rs9633334	0.84[CHD][hapmap]
rs968304	1.00[CHB][hapmap];0.81[CHD][hapmap];0.84[ASN][1000 genomes]
rs9887857	0.82[CHB][hapmap]
rs9988604	0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	esv17936	chr1:169112379-169112882	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12691502	NME7	cis	Artery Tibial	GTEx
rs12691502	MGST3	cis	parietal	SCAN
rs12691502	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs12691502	ALDH9A1	cis	cerebellum	SCAN

Chromatin state (count:38 , 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	chr1:169111800-169113400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:169111800-169113800	Enhancers	HepG2	liver
32	chr1:169112000-169112800	Enhancers	Psoas Muscle	Psoas
33	chr1:169112400-169113600	Enhancers	A549	lung
34	chr1:169112600-169112800	Weak transcription	Brain Angular Gyrus	brain
35	chr1:169112600-169112800	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr1:169112600-169112800	Enhancers	K562	blood
37	chr1:169112600-169114200	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr1:169112600-169118400	Enhancers	Stomach Mucosa	stomach

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