Variant report

Variant	rs12403586
Chromosome Location	chr1:212586736-212586737
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr1:212586575-212589515	K562	blood:	n/a	chr1:212587985-212587994 chr1:212589466-212589475
2	MXI1	chr1:212586634-212588790	SK-N-SH	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212458597..212460542-chr1:212586367..212588357,2	MCF-7	breast:
2	chr1:212550848..212553114-chr1:212586010..212588532,2	MCF-7	breast:
3	chr1:212586222..212588940-chr1:212781343..212783037,2	K562	blood:
4	chr1:212586060..212592297-chr1:212603893..212609565,9	MCF-7	breast:
5	chr1:212457988..212460167-chr1:212585002..212587734,2	MCF-7	breast:
6	chr1:212585974..212594847-chr1:212598812..212609579,19	K562	blood:
7	chr1:212586665..212588349-chr1:212964322..212966191,2	MCF-7	breast:

No data

Variant related genes	Relation type
TMEM206	TF binding region
ENSG00000203705	Chromatin interaction
ENSG00000066027	Chromatin interaction
ENSG00000117697	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000117691	Chromatin interaction
ENSG00000065600	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1056985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10863955	0.93[CEU][hapmap]
rs10863965	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11119886	0.93[CEU][hapmap]
rs11119891	1.00[CEU][hapmap]
rs11119910	0.91[CEU][hapmap]
rs11119918	1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[ASN][1000 genomes]
rs11119927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11119932	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11119934	0.93[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11119940	1.00[MKK][hapmap]
rs11119941	1.00[MKK][hapmap]
rs11119951	1.00[MKK][hapmap]
rs11119953	1.00[MKK][hapmap]
rs12031941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12033979	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12118709	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12119779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12128123	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12128965	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12133582	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12133636	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12134599	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs12136095	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12138533	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12140158	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12141427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12143853	1.00[CEU][hapmap]
rs12145170	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12145377	0.92[CEU][hapmap]
rs12145484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12239580	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12561785	0.83[EUR][1000 genomes]
rs1342152	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1388033	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1388034	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs14123	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17018777	0.93[CEU][hapmap]
rs17018847	1.00[CEU][hapmap]
rs17018853	1.00[CEU][hapmap]
rs17666015	0.86[EUR][1000 genomes]
rs1808986	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1826214	1.00[MKK][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs2166155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2298115	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs3754142	0.83[CHB][hapmap]
rs3754144	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3767867	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs3767868	1.00[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MKK][hapmap];0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3767872	0.83[AFR][1000 genomes]
rs3820513	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4338424	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4548507	0.94[ASN][1000 genomes]
rs4951447	1.00[MKK][hapmap]
rs4951448	1.00[MKK][hapmap]
rs4951596	0.93[ASN][1000 genomes]
rs4951597	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59001230	0.83[AFR][1000 genomes]
rs61828751	0.83[EUR][1000 genomes]
rs74138154	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs765364	0.82[JPT][hapmap]
rs903119	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
7	esv1828436	chr1:212577765-212591863	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv873156	chr1:212585092-212646225	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12403586	PPP2R5A	cis	Whole Blood	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212556800-212587600	Weak transcription	Small Intestine	intestine
2	chr1:212579800-212587000	Weak transcription	Right Atrium	heart
3	chr1:212580600-212587200	Weak transcription	HSMMtube	muscle
4	chr1:212580800-212587000	Weak transcription	NHDF-Ad	bronchial
5	chr1:212583200-212586800	Weak transcription	HMEC	breast
6	chr1:212583200-212587000	Weak transcription	Fetal Heart	heart
7	chr1:212583200-212587000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:212583400-212586800	Weak transcription	HUVEC	blood vessel
9	chr1:212583600-212586800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:212583600-212587000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr1:212583600-212587000	Weak transcription	Hela-S3	cervix
12	chr1:212583800-212587000	Weak transcription	Right Ventricle	heart
13	chr1:212583800-212587000	Weak transcription	A549	lung
14	chr1:212583800-212587000	Weak transcription	NH-A	brain
15	chr1:212584000-212587000	Weak transcription	Fetal Kidney	kidney
16	chr1:212584000-212587200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:212584000-212587400	Weak transcription	Ovary	ovary
18	chr1:212584200-212586800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:212584200-212586800	Weak transcription	Adipose Nuclei	Adipose
20	chr1:212584200-212586800	Weak transcription	Esophagus	oesophagus
21	chr1:212584200-212586800	Weak transcription	Placenta	Placenta
22	chr1:212584200-212587000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:212584200-212587000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:212584200-212587000	Weak transcription	NHLF	lung
25	chr1:212584200-212587200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:212584200-212587200	Weak transcription	Fetal Lung	lung
27	chr1:212584200-212587200	Weak transcription	Osteobl	bone
28	chr1:212584400-212587000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:212584400-212587000	Weak transcription	Liver	Liver
30	chr1:212584400-212587000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:212584400-212587200	Weak transcription	Fetal Intestine Large	intestine
32	chr1:212584400-212587200	Weak transcription	Gastric	stomach
33	chr1:212584600-212587200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:212584800-212586800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:212584800-212586800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:212584800-212586800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:212584800-212586800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:212584800-212586800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:212584800-212586800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:212584800-212586800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr1:212584800-212586800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:212584800-212587000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:212584800-212587000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:212584800-212587000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:212584800-212587000	Weak transcription	Left Ventricle	heart
46	chr1:212584800-212587200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:212585000-212586800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:212585000-212586800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr1:212585000-212586800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:212585000-212586800	Weak transcription	Lung	lung

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