Variant report

Variant	rs399429
Chromosome Location	chr1:212389801-212389802
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212389745..212391730-chr1:212393335..212395896,2	K562	blood:
2	chr1:212386087..212387745-chr1:212388194..212390712,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1011232	0.82[CHB][hapmap]
rs1056985	0.93[CEU][hapmap]
rs10779573	0.84[AMR][1000 genomes]
rs10863955	1.00[CEU][hapmap];0.96[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10863957	0.81[CHB][hapmap]
rs11119874	0.84[AMR][1000 genomes]
rs11119886	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11119888	0.81[CHB][hapmap]
rs11119891	0.93[CEU][hapmap]
rs11119910	0.82[CEU][hapmap]
rs12022111	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12119779	0.93[CEU][hapmap]
rs12124065	0.89[ASN][1000 genomes]
rs12127954	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs12128965	0.93[CEU][hapmap]
rs12133134	0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs12134060	0.81[AMR][1000 genomes]
rs12135257	0.85[AMR][1000 genomes]
rs12136095	0.93[CEU][hapmap]
rs12136808	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12137322	0.82[AMR][1000 genomes]
rs12141427	0.93[CEU][hapmap]
rs12142929	0.85[AMR][1000 genomes]
rs12143853	1.00[CEU][hapmap]
rs12145030	0.82[AMR][1000 genomes]
rs12145377	0.83[CEU][hapmap]
rs12145484	0.93[CEU][hapmap]
rs12403586	0.93[CEU][hapmap]
rs12407827	0.84[AMR][1000 genomes]
rs1342152	0.93[CEU][hapmap]
rs14123	0.93[CEU][hapmap]
rs1493602	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17018685	0.84[AMR][1000 genomes]
rs17018777	1.00[CEU][hapmap];0.96[CHB][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17018847	0.92[CEU][hapmap]
rs17018853	0.92[CEU][hapmap]
rs17663598	0.82[EUR][1000 genomes]
rs2358446	0.83[EUR][1000 genomes]
rs3820513	0.93[CEU][hapmap]
rs4418675	0.84[AMR][1000 genomes]
rs4951446	1.00[AFR][1000 genomes]
rs4951580	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs884923	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs903119	0.93[CEU][hapmap]
rs9793334	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9793974	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs399429	PPP2R5A	cis	Thyroid	GTEx
rs399429	PPP2R5A	cis	Whole Blood	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212368800-212391000	Weak transcription	Thymus	Thymus
2	chr1:212379600-212391600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:212381800-212391200	Weak transcription	Right Atrium	heart
4	chr1:212382800-212391000	Weak transcription	Stomach Mucosa	stomach
5	chr1:212383000-212393000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:212383400-212394600	Weak transcription	Left Ventricle	heart
7	chr1:212386400-212391200	Weak transcription	Fetal Kidney	kidney
8	chr1:212387600-212391200	Weak transcription	Spleen	Spleen
9	chr1:212387800-212390800	Weak transcription	Adipose Nuclei	Adipose
10	chr1:212388000-212390800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:212388600-212391000	Weak transcription	Fetal Thymus	thymus
12	chr1:212388600-212392400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:212388600-212393000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:212388600-212393200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:212388800-212391000	Weak transcription	Fetal Intestine Small	intestine
16	chr1:212388800-212391200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:212389000-212391000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:212389000-212391200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:212389000-212392000	Weak transcription	K562	blood
20	chr1:212389000-212393000	Weak transcription	Fetal Intestine Large	intestine
21	chr1:212389600-212391800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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