Variant report

Variant	rs2298115
Chromosome Location	chr1:212474910-212474911
allele	C/T
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	chr1:212474770-212475231	MCF10A-Er-Src	breast:	n/a	chr1:212474880-212474892
2	STAT3	chr1:212474831-212475176	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr1:212474770-212475234	MCF10A-Er-Src	breast:	n/a	chr1:212474880-212474892
4	E2F4	chr1:212474881-212475147	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr1:212474799-212474997	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr1:212474877-212475272	MCF10A-Er-Src	breast:	n/a	chr1:212474880-212474892
7	FOS	chr1:212474828-212475174	MCF10A-Er-Src	breast:	n/a	chr1:212474880-212474892

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212467247..212471909-chr1:212472711..212476183,6	K562	blood:

Variant related genes	Relation type
PPP2R5A	TF binding region
ENSG00000230063	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1056985	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10863956	1.00[AFR][1000 genomes]
rs10863965	0.86[CEU][hapmap];0.95[CHB][hapmap]
rs11119886	1.00[AFR][1000 genomes]
rs11119891	0.86[CEU][hapmap];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];0.99[ASN][1000 genomes]
rs11119908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119918	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11119927	0.82[EUR][1000 genomes]
rs11119932	0.86[CEU][hapmap];0.95[CHB][hapmap]
rs11119934	0.93[CEU][hapmap];0.95[CHB][hapmap]
rs12118709	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[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	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs12124582	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12128123	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12128965	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12133582	0.86[CEU][hapmap];0.95[CHB][hapmap]
rs12133636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12136095	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12137798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12138533	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12140158	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12141427	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs12143853	0.82[CEU][hapmap];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];0.86[ASN][1000 genomes]
rs12145484	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12146141	1.00[AFR][1000 genomes]
rs12239580	1.00[CHB][hapmap]
rs12403586	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs12561785	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[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	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs14123	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1493601	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17018847	0.84[CEU][hapmap]
rs17018853	0.84[CEU][hapmap]
rs2166155	1.00[CHB][hapmap]
rs2236598	0.90[ASN][1000 genomes]
rs3754142	0.83[CHB][hapmap]
rs3754144	0.95[CHB][hapmap]
rs3767867	1.00[CHB][hapmap]
rs3767868	0.95[CHB][hapmap]
rs3820513	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs4951597	0.86[CEU][hapmap];0.95[CHB][hapmap]
rs903119	0.86[CEU][hapmap];1.00[AFR][1000 genomes]

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	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	esv1839887	chr1:212457414-212478047	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2298115	PPP2R5A	cis	Whole Blood	GTEx
rs2298115	PPP2R5A	cis	Thyroid	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212460200-212489200	Weak transcription	Spleen	Spleen
2	chr1:212461000-212476200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:212464200-212483000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:212464800-212480200	Weak transcription	Lung	lung
5	chr1:212464800-212483800	Weak transcription	Pancreas	Pancrea
6	chr1:212464800-212506400	Weak transcription	Esophagus	oesophagus
7	chr1:212465000-212480200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:212465400-212475000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:212465400-212482800	Weak transcription	Fetal Lung	lung
10	chr1:212465800-212483200	Weak transcription	Dnd41	blood
11	chr1:212466200-212506400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:212466600-212479400	Weak transcription	NHEK	skin
13	chr1:212466600-212482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:212466600-212503000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:212467000-212480800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:212467200-212475000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:212467200-212481800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr1:212467400-212480200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr1:212467400-212482800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:212467400-212526000	Weak transcription	A549	lung
21	chr1:212467600-212482800	Weak transcription	HepG2	liver
22	chr1:212468800-212476000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:212468800-212478200	Weak transcription	Fetal Intestine Small	intestine
24	chr1:212469000-212480200	Weak transcription	Fetal Intestine Large	intestine
25	chr1:212469000-212483200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:212469000-212483400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:212469600-212475000	Weak transcription	Adipose Nuclei	Adipose
28	chr1:212470000-212476000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:212470000-212476400	Weak transcription	K562	blood
30	chr1:212470000-212481800	Weak transcription	Thymus	Thymus
31	chr1:212470400-212481200	Weak transcription	Primary T cells from cord blood	blood
32	chr1:212470800-212482600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:212471000-212475000	Weak transcription	Brain Angular Gyrus	brain
34	chr1:212472600-212475200	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr1:212472600-212478200	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr1:212473000-212475200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:212473400-212477000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:212473400-212477800	Weak transcription	Psoas Muscle	Psoas
39	chr1:212473400-212483800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:212473600-212478800	Weak transcription	Small Intestine	intestine
41	chr1:212474000-212477600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr1:212474200-212475400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:212474200-212475600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:212474200-212475600	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr1:212474200-212476600	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr1:212474200-212484000	Weak transcription	Primary B cells from cord blood	blood
47	chr1:212474200-212502800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:212474400-212475200	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr1:212474400-212475200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:212474400-212475200	Enhancers	Brain Inferior Temporal Lobe	brain

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