Variant report

Variant	rs12139040
Chromosome Location	chr1:179969684-179969685
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179845220..179846816-chr1:179967799..179969791,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TOR1AIP2-6	chr1:179969573-179969943	NONHSAT008237

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10913920	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12116940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118265	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12119130	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125245	0.85[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125592	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126496	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12126967	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127784	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129115	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130397	0.84[EUR][1000 genomes]
rs12130673	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131200	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133136	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135828	0.84[EUR][1000 genomes]
rs12138429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140589	0.84[EUR][1000 genomes]
rs12140622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141134	1.00[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144328	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144346	0.82[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144352	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184265	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855070	0.84[EUR][1000 genomes]
rs17299006	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371159	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371308	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1801795	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856049	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59132689	0.82[EUR][1000 genomes]
rs73032390	0.82[EUR][1000 genomes]
rs9701232	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9701237	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv466228	chr1:179944901-180067988	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv548340	chr1:179944901-180067988	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv520322	chr1:179944901-180071987	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv548341	chr1:179945390-180067914	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv520278	chr1:179945390-180093066	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv548342	chr1:179958809-180067988	Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv548343	chr1:179958809-180071987	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv548344	chr1:179960787-180071987	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12139040	CEP350	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179938000-179983200	Weak transcription	Brain Germinal Matrix	brain
2	chr1:179938600-179975800	Weak transcription	Thymus	Thymus
3	chr1:179938600-179983200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:179938600-179984600	Weak transcription	Lung	lung
5	chr1:179939000-179989000	Weak transcription	Gastric	stomach
6	chr1:179939800-179974800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:179941400-180031800	Weak transcription	Spleen	Spleen
8	chr1:179946400-179972800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:179946400-179983000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:179946400-179989200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:179946600-179983200	Weak transcription	Brain Angular Gyrus	brain
12	chr1:179947800-179989400	Weak transcription	Small Intestine	intestine
13	chr1:179948400-179971800	Weak transcription	Fetal Heart	heart
14	chr1:179948600-179983200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:179949400-179980600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:179950000-179980600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:179951400-179972200	Weak transcription	Psoas Muscle	Psoas
18	chr1:179951400-179974600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr1:179951800-179974800	Weak transcription	Hela-S3	cervix
20	chr1:179953600-179971400	Weak transcription	HMEC	breast
21	chr1:179954200-179975400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:179954600-179975600	Weak transcription	Fetal Kidney	kidney
23	chr1:179954800-179971200	Weak transcription	NHEK	skin
24	chr1:179955000-179989200	Weak transcription	Aorta	Aorta
25	chr1:179955800-179983000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:179956400-179970000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:179956800-179989400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:179957000-179975800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:179957800-179969800	Weak transcription	NHDF-Ad	bronchial
30	chr1:179957800-179972400	Weak transcription	Brain Anterior Caudate	brain
31	chr1:179958600-179971800	Weak transcription	HSMMtube	muscle
32	chr1:179958600-179991600	Weak transcription	Fetal Brain Male	brain
33	chr1:179958800-179978000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:179959000-179970000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:179959200-179983200	Weak transcription	NHLF	lung
36	chr1:179959600-179983000	Weak transcription	Colonic Mucosa	Colon
37	chr1:179962000-179989200	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:179962400-179983200	Weak transcription	A549	lung
39	chr1:179962800-179970800	Strong transcription	Dnd41	blood
40	chr1:179963600-179975800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:179963800-179970400	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:179964000-179989200	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr1:179964000-180014200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:179964200-179975400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:179964400-179971400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:179964400-179984600	Weak transcription	HUVEC	blood vessel
47	chr1:179964600-179984200	Weak transcription	Fetal Intestine Small	intestine
48	chr1:179965000-179978000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:179965800-180013200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:179966000-179970200	Strong transcription	Muscle Satellite Cultured Cells	--

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