Variant report

Variant	rs12125245
Chromosome Location	chr1:180000542-180000543
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179998094..180000667-chr1:180001189..180004534,3	MCF-7	breast:
2	chr1:179997127..180001716-chr1:180009044..180014069,5	MCF-7	breast:
3	chr1:179998356..180000949-chr1:180019994..180021642,2	K562	blood:
4	chr1:179999019..180000801-chr1:180002803..180004316,2	K562	blood:

Variant related genes	Relation type
ENSG00000135837	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10442618	0.84[EUR][1000 genomes]
rs10913920	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12116940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118265	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12119130	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120418	0.83[EUR][1000 genomes]
rs12123139	0.83[EUR][1000 genomes]
rs12124265	0.84[EUR][1000 genomes]
rs12125592	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125893	0.84[EUR][1000 genomes]
rs12126496	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126967	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127784	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129115	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130673	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131200	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133136	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141134	0.89[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs12144328	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144346	1.00[GIH][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144352	0.89[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184265	0.89[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855107	0.83[EUR][1000 genomes]
rs16855110	0.84[EUR][1000 genomes]
rs16855125	0.84[EUR][1000 genomes]
rs16855130	0.84[EUR][1000 genomes]
rs17299006	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371159	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371308	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1801795	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856049	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4266842	0.84[EUR][1000 genomes]
rs4278337	0.84[EUR][1000 genomes]
rs59132689	0.82[EUR][1000 genomes]
rs61242295	0.83[EUR][1000 genomes]
rs73032390	0.82[EUR][1000 genomes]
rs73032397	0.84[EUR][1000 genomes]
rs73034408	0.84[EUR][1000 genomes]
rs9701232	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9701237	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv3755	chr1:179998860-180043554	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
13	nsv1000698	chr1:179999669-180042521	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12125245	CEP350	Cis_1M	lymphoblastoid	RTeQTL
rs12125245	RALGPS2	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179941400-180031800	Weak transcription	Spleen	Spleen
2	chr1:179964000-180014200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:179965800-180013200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:179970800-180076800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr1:179973000-180010800	Weak transcription	Psoas Muscle	Psoas
6	chr1:179976200-180063600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:179979600-180002000	Strong transcription	Fetal Intestine Large	intestine
8	chr1:179979800-180008400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:179980200-180007800	Strong transcription	Primary B cells from cord blood	blood
10	chr1:179980400-180027400	Strong transcription	Dnd41	blood
11	chr1:179980600-180008000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:179981000-180027200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr1:179981000-180059000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:179981600-180012000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:179983600-180083400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:179985600-180024800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:179989000-180008800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:179989800-180034200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:179990000-180010200	Weak transcription	NHEK	skin
20	chr1:179990000-180012000	Weak transcription	Gastric	stomach
21	chr1:179990000-180012200	Weak transcription	Stomach Mucosa	stomach
22	chr1:179990000-180025600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:179990200-180025400	Weak transcription	Pancreas	Pancrea
24	chr1:179990600-180002600	Weak transcription	A549	lung
25	chr1:179990800-180003600	Weak transcription	Small Intestine	intestine
26	chr1:179992400-180001000	Weak transcription	Left Ventricle	heart
27	chr1:179992400-180009200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:179992400-180009200	Weak transcription	HMEC	breast
29	chr1:179992400-180012000	Weak transcription	Right Ventricle	heart
30	chr1:179992400-180031400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:179992400-180032200	Weak transcription	Esophagus	oesophagus
32	chr1:179992600-180000800	Weak transcription	HepG2	liver
33	chr1:179992600-180010800	Weak transcription	Colonic Mucosa	Colon
34	chr1:179993000-180010000	Weak transcription	Fetal Brain Male	brain
35	chr1:179993200-180002800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr1:179993800-180000800	Weak transcription	Fetal Kidney	kidney
37	chr1:179993800-180005000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:179993800-180010800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:179994000-180005400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:179995000-180000600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr1:179995000-180003000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:179995000-180003000	Weak transcription	Ovary	ovary
43	chr1:179995000-180003200	Weak transcription	Brain Germinal Matrix	brain
44	chr1:179995400-180003000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:179995600-180003000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:179996000-180002800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:179996200-180003000	Weak transcription	Fetal Heart	heart
48	chr1:179996400-180002600	Weak transcription	Brain Angular Gyrus	brain
49	chr1:179996400-180003000	Weak transcription	Brain Anterior Caudate	brain
50	chr1:179996400-180003400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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