Variant report

Variant	rs3820513
Chromosome Location	chr1:212589557-212589558
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SREBP1	chr1:212587176-212589923	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212588338..212589858-chr1:212645243..212647080,2	K562	blood:
2	chr1:212587143..212589756-chr1:212965630..212967810,2	K562	blood:
3	chr1:212586060..212592297-chr1:212603893..212609565,9	MCF-7	breast:
4	chr1:212588056..212590074-chr1:212779163..212783567,3	K562	blood:
5	chr1:212587912..212590110-chr1:212604889..212609190,4	K562	blood:
6	chr1:212526286..212528256-chr1:212589016..212590996,2	K562	blood:
7	chr1:212585974..212594847-chr1:212598812..212609579,19	K562	blood:
8	chr1:212589362..212592084-chr1:212630605..212632407,2	K562	blood:

No data

Variant related genes	Relation type
TMEM206	TF binding region
ENSG00000162772	Chromatin interaction
ENSG00000203705	Chromatin interaction
ENSG00000117691	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];0.95[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];0.80[CHD][hapmap];0.82[ASN][1000 genomes]
rs11119927	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];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11119934	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[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[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];0.95[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];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[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];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12239580	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12403586	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]
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];0.80[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	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];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs3767868	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[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]
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];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[AFR][1000 genomes];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
rs3820513	PPP2R5A	cis	Whole Blood	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212588400-212590200	Enhancers	Primary hematopoietic stem cells	blood
2	chr1:212588400-212590600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:212588600-212590200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr1:212588600-212590200	Enhancers	Pancreas	Pancrea
5	chr1:212588600-212595000	Weak transcription	Right Atrium	heart
6	chr1:212588800-212590000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:212588800-212590800	Enhancers	Brain Angular Gyrus	brain
8	chr1:212588800-212591800	Weak transcription	Fetal Intestine Large	intestine
9	chr1:212589000-212590200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:212589000-212590400	Enhancers	Brain Anterior Caudate	brain
11	chr1:212589000-212590600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:212589000-212591000	Enhancers	Brain Cingulate Gyrus	brain
13	chr1:212589000-212591000	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr1:212589000-212591400	Enhancers	Brain Substantia Nigra	brain
15	chr1:212589000-212591800	Weak transcription	Fetal Intestine Small	intestine
16	chr1:212589000-212592600	Enhancers	K562	blood
17	chr1:212589200-212590000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:212589200-212590400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:212589200-212590400	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr1:212589200-212590600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:212589200-212590600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:212589200-212591600	Weak transcription	Spleen	Spleen
23	chr1:212589200-212593600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:212589200-212593800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:212589400-212590400	Enhancers	Brain Hippocampus Middle	brain
26	chr1:212589400-212591800	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr1:212589400-212591800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr1:212589400-212593800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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