Variant report

Variant	rs12127784
Chromosome Location	chr1:180078549-180078550
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	chr1:180078096..180081718-chr1:180085616..180088011,3	MCF-7	breast:
2	chr1:180077063..180078624-chr1:180082049..180084271,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10913920	1.00[ASN][1000 genomes]
rs12116940	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118265	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118985	0.84[EUR][1000 genomes]
rs12119130	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12121834	0.84[EUR][1000 genomes]
rs12121845	0.84[EUR][1000 genomes]
rs12125245	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125556	0.84[EUR][1000 genomes]
rs12125592	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125693	0.84[EUR][1000 genomes]
rs12126496	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126967	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129115	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130479	0.82[EUR][1000 genomes]
rs12130489	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12130673	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12131200	1.00[ASN][1000 genomes]
rs12133136	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12134536	0.84[EUR][1000 genomes]
rs12138201	0.84[EUR][1000 genomes]
rs12138429	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138974	0.83[EUR][1000 genomes]
rs12139040	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139761	0.81[EUR][1000 genomes]
rs12140235	0.84[EUR][1000 genomes]
rs12140622	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140868	0.84[EUR][1000 genomes]
rs12141134	1.00[ASN][1000 genomes]
rs12144328	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144346	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144352	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144853	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184265	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184270	0.82[EUR][1000 genomes]
rs16843139	0.84[EUR][1000 genomes]
rs16855268	0.83[EUR][1000 genomes]
rs16855270	0.84[EUR][1000 genomes]
rs17299006	1.00[ASN][1000 genomes]
rs17371159	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371267	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17371308	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1801795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856049	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4460595	0.82[EUR][1000 genomes]
rs60972670	0.84[EUR][1000 genomes]
rs73034486	0.82[EUR][1000 genomes]
rs9701232	1.00[ASN][1000 genomes]
rs9701237	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
3	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
4	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	nsv1012558	chr1:180027960-180217613	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv535218	chr1:180027960-180217613	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv497930	chr1:180031321-180220723	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv533073	chr1:180031328-180217612	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv916937	chr1:180031328-180220685	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12127784	CEP350	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179983600-180083400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:180000800-180083400	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:180002400-180085000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:180013000-180080000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:180029600-180084800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:180040800-180082200	Strong transcription	Primary B cells from peripheral blood	blood
7	chr1:180042000-180082600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:180048800-180082200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr1:180052800-180082600	Strong transcription	Fetal Thymus	thymus
10	chr1:180052800-180085800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:180053000-180083000	Strong transcription	Liver	Liver
12	chr1:180054000-180082600	Strong transcription	Dnd41	blood
13	chr1:180054600-180079400	Weak transcription	Fetal Brain Male	brain
14	chr1:180057600-180082600	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:180057600-180082800	Strong transcription	Adipose Nuclei	Adipose
16	chr1:180062600-180079600	Weak transcription	Fetal Heart	heart
17	chr1:180064400-180079400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:180065000-180079400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:180065000-180079400	Weak transcription	Psoas Muscle	Psoas
20	chr1:180065000-180079400	Weak transcription	NHLF	lung
21	chr1:180065000-180080000	Weak transcription	NHEK	skin
22	chr1:180065000-180080200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:180065200-180078600	Weak transcription	Brain Angular Gyrus	brain
24	chr1:180065400-180080000	Weak transcription	HMEC	breast
25	chr1:180066200-180079400	Weak transcription	Colonic Mucosa	Colon
26	chr1:180066200-180079400	Weak transcription	Stomach Mucosa	stomach
27	chr1:180066200-180082200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:180066400-180079600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr1:180066400-180080000	Weak transcription	Brain Germinal Matrix	brain
30	chr1:180066400-180080200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:180066600-180079200	Weak transcription	NH-A	brain
32	chr1:180066600-180079400	Weak transcription	Brain Anterior Caudate	brain
33	chr1:180068000-180079600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:180068200-180078800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:180068200-180080200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr1:180068600-180079000	Weak transcription	Hela-S3	cervix
37	chr1:180068800-180082000	Strong transcription	Fetal Muscle Leg	muscle
38	chr1:180069000-180079400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:180069200-180082000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:180069400-180082400	Strong transcription	Primary T cells from cord blood	blood
41	chr1:180069800-180078600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:180070600-180079200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:180071000-180079400	Weak transcription	Aorta	Aorta
44	chr1:180071200-180079000	Weak transcription	Fetal Brain Female	brain
45	chr1:180071200-180079400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:180071200-180079400	Weak transcription	HSMM	muscle
47	chr1:180071200-180080200	Weak transcription	Right Ventricle	heart
48	chr1:180071400-180079200	Weak transcription	Esophagus	oesophagus
49	chr1:180071400-180084400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:180071600-180080200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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