Variant report

Variant	rs11119927
Chromosome Location	chr1:212569336-212569337
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212569162..212572404-chr1:212781980..212783777,4	K562	blood:

Variant related genes	Relation type
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1056985	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10863965	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11119907	0.82[EUR][1000 genomes]
rs11119908	0.82[EUR][1000 genomes]
rs11119910	0.82[EUR][1000 genomes]
rs11119918	0.87[ASN][1000 genomes]
rs11119932	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11119934	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12031941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12033979	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12118709	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12119779	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128123	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12128965	0.82[EUR][1000 genomes]
rs12129267	0.82[EUR][1000 genomes]
rs12133582	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12133636	0.90[ASN][1000 genomes]
rs12134599	0.91[ASN][1000 genomes]
rs12136095	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12137798	0.82[EUR][1000 genomes]
rs12138533	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12140158	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12141427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143853	0.80[EUR][1000 genomes]
rs12145170	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12145484	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12239580	0.94[ASN][1000 genomes]
rs12403586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12561785	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1388033	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1388034	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs14123	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17666015	0.83[EUR][1000 genomes]
rs1808986	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166155	0.94[ASN][1000 genomes]
rs2298115	0.82[EUR][1000 genomes]
rs3754144	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3767867	0.99[ASN][1000 genomes]
rs3767868	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3767872	0.83[AFR][1000 genomes]
rs3820513	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4338424	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4548507	1.00[ASN][1000 genomes]
rs4951596	0.87[ASN][1000 genomes]
rs4951597	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59001230	0.83[AFR][1000 genomes]
rs74138154	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11119927	PPP2R5A	cis	Whole Blood	GTEx
rs11119927	C1orf75	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212526800-212582800	Weak transcription	Fetal Brain Male	brain
2	chr1:212528400-212583000	Weak transcription	Fetal Kidney	kidney
3	chr1:212534000-212570200	Weak transcription	HSMM	muscle
4	chr1:212534400-212570600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:212538000-212571000	Weak transcription	NH-A	brain
6	chr1:212540400-212575400	Weak transcription	HUVEC	blood vessel
7	chr1:212553200-212569400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:212553200-212578400	Weak transcription	K562	blood
9	chr1:212556800-212587600	Weak transcription	Small Intestine	intestine
10	chr1:212558600-212578800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:212558600-212580000	Weak transcription	Left Ventricle	heart
12	chr1:212560200-212578400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:212560400-212570600	Weak transcription	NHLF	lung
14	chr1:212560400-212580200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:212560600-212570000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:212560600-212570200	Weak transcription	Brain Substantia Nigra	brain
17	chr1:212560600-212578200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:212560600-212578800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:212560600-212580200	Weak transcription	HSMMtube	muscle
20	chr1:212560600-212582000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:212560600-212582000	Weak transcription	Gastric	stomach
22	chr1:212561000-212575400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:212561000-212578000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr1:212561000-212579800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:212561000-212579800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:212561000-212580000	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:212561000-212582400	Weak transcription	Aorta	Aorta
28	chr1:212561200-212572000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:212562000-212570200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:212562000-212578400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:212562400-212570600	Weak transcription	NHEK	skin
32	chr1:212562600-212571200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:212563600-212570000	Weak transcription	GM12878-XiMat	blood
34	chr1:212563800-212570000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:212563800-212570600	Weak transcription	Primary T cells from cord blood	blood
36	chr1:212564000-212570000	Weak transcription	Dnd41	blood
37	chr1:212564200-212578800	Weak transcription	Esophagus	oesophagus
38	chr1:212564400-212570800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:212564400-212575400	Weak transcription	Thymus	Thymus
40	chr1:212564600-212569800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:212564600-212569800	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr1:212564600-212570200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:212564600-212570600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:212564600-212570600	Weak transcription	Fetal Thymus	thymus
45	chr1:212564600-212576200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:212564600-212577800	Weak transcription	Spleen	Spleen
47	chr1:212564600-212578600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:212564600-212579800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:212564800-212569400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:212564800-212570400	Weak transcription	Primary hematopoietic stem cells	blood

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