Variant report

Variant	rs12129267
Chromosome Location	chr1:212485375-212485376
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr1:212485201-212485819	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr1:212485210-212485762	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr1:212485195-212485772	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr1:212485236-212485805	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr1:212485194-212485815	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212458567..212461041-chr1:212484616..212487117,2	MCF-7	breast:
2	chr1:212480848..212483248-chr1:212485373..212487315,2	K562	blood:

Variant related genes	Relation type
ENSG00000225338	TF binding region
ENSG00000066027	Chromatin interaction
ENSG00000225338	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1056985	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10863956	1.00[AFR][1000 genomes]
rs11119886	1.00[AFR][1000 genomes]
rs11119891	1.00[AFR][1000 genomes]
rs11119893	1.00[AFR][1000 genomes]
rs11119903	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11119907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11119908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119918	0.91[ASN][1000 genomes]
rs11119927	0.82[EUR][1000 genomes]
rs12118709	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12118732	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12119779	0.82[EUR][1000 genomes]
rs12124582	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12128123	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12128965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12133636	0.88[ASN][1000 genomes]
rs12134074	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12134599	0.87[ASN][1000 genomes]
rs12136095	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12137798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12138533	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12140158	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12141427	0.82[EUR][1000 genomes]
rs12143853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12145170	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12145484	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12146141	1.00[AFR][1000 genomes]
rs12561785	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12562618	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1342152	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs14123	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1493601	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2236598	0.89[ASN][1000 genomes]
rs2298115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs903119	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers 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	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv873155	chr1:212449195-212502157	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv1806604	chr1:212468974-212505860	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12129267	PPP2R5A	cis	Whole Blood	GTEx
rs12129267	PPP2R5A	cis	Thyroid	GTEx
rs12129267	C1orf75	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212460200-212489200	Weak transcription	Spleen	Spleen
2	chr1:212464800-212506400	Weak transcription	Esophagus	oesophagus
3	chr1:212466200-212506400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:212466600-212503000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:212467400-212526000	Weak transcription	A549	lung
6	chr1:212474200-212502800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:212474600-212489200	Weak transcription	Gastric	stomach
8	chr1:212475200-212487000	Weak transcription	HSMMtube	muscle
9	chr1:212475400-212487000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:212475600-212488600	Weak transcription	Fetal Heart	heart
11	chr1:212478200-212495800	Weak transcription	Fetal Thymus	thymus
12	chr1:212479200-212525400	Weak transcription	Aorta	Aorta
13	chr1:212479600-212489000	Weak transcription	Small Intestine	intestine
14	chr1:212479600-212489200	Weak transcription	Stomach Mucosa	stomach
15	chr1:212480400-212485400	Weak transcription	HMEC	breast
16	chr1:212480600-212489400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:212480800-212488400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:212481600-212485800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:212481600-212488600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr1:212482600-212486000	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr1:212482600-212486200	Weak transcription	Fetal Muscle Leg	muscle
22	chr1:212482600-212488800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:212483400-212488000	Enhancers	NHDF-Ad	bronchial
24	chr1:212483400-212489400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:212483800-212487800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:212483800-212489200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr1:212484000-212485400	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:212484000-212485400	Weak transcription	Fetal Lung	lung
29	chr1:212484000-212485800	Weak transcription	Ovary	ovary
30	chr1:212484000-212486000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:212484000-212487600	Strong transcription	Primary B cells from cord blood	blood
32	chr1:212484000-212487600	Enhancers	Osteobl	bone
33	chr1:212484000-212503000	Weak transcription	Fetal Stomach	stomach
34	chr1:212484000-212506600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:212484200-212485400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:212484200-212486600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:212484200-212487400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:212484200-212487400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:212484200-212487800	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:212484200-212488600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:212484200-212488600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:212484200-212489000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:212484200-212489200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:212484200-212493400	Weak transcription	K562	blood
45	chr1:212484200-212507000	Weak transcription	HepG2	liver
46	chr1:212484400-212485400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:212484400-212485400	Weak transcription	Brain Anterior Caudate	brain
48	chr1:212484400-212485400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:212484400-212485400	Weak transcription	GM12878-XiMat	blood
50	chr1:212484400-212487200	Weak transcription	Primary monocytes fromperipheralblood	blood

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