Variant report

Variant	rs11265251
Chromosome Location	chr1:154157090-154157091
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr1:154156993-154157206	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr1:154156828-154157204	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr1:154156837-154157144	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154151605..154157694-chr1:154191153..154195788,18	MCF-7	breast:
2	chr1:154155037..154157341-chr1:154243497..154245632,3	MCF-7	breast:
3	chr1:154153141..154174161-chr1:154187746..154196033,47	MCF-7	breast:
4	chr1:154145134..154153289-chr1:154153487..154160631,22	K562	blood:
5	chr1:154153643..154157449-chr1:154190048..154195510,8	K562	blood:
6	chr1:154156233..154161758-chr1:154162933..154167291,6	K562	blood:
7	chr1:153938202..153942686-chr1:154154566..154158952,5	MCF-7	breast:
8	chr1:154155019..154156953-chr1:154157061..154158850,3	MCF-7	breast:
9	chr1:154155278..154160143-chr1:154165338..154167782,4	K562	blood:
10	chr1:154154241..154157353-chr1:154161640..154168172,9	MCF-7	breast:
11	chr1:154149113..154161877-chr1:154185436..154196776,24	K562	blood:
12	chr1:154154597..154158912-chr1:154243474..154246502,4	K562	blood:

No data

Variant related genes	Relation type
TPM3	TF binding region
ENSG00000143569	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000273026	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000143575	Chromatin interaction
ENSG00000215938	Chromatin interaction
ENSG00000143612	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10158820	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1044013	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10797047	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11265238	0.91[JPT][hapmap]
rs11265425	0.95[JPT][hapmap]
rs11802893	0.86[JPT][hapmap]
rs1194593	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1194596	0.82[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12023901	0.82[ASN][1000 genomes]
rs12025237	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs12026177	0.91[JPT][hapmap]
rs12026475	0.83[EUR][1000 genomes]
rs12026615	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs12027999	0.82[ASN][1000 genomes]
rs12028554	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12028949	0.91[JPT][hapmap]
rs12029331	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12062977	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12733060	0.83[ASN][1000 genomes]
rs12738393	0.83[ASN][1000 genomes]
rs16835846	0.87[JPT][hapmap]
rs16835852	0.87[JPT][hapmap]
rs1760802	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1986709	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2220390	0.80[YRI][hapmap]
rs2274993	0.83[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2340473	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2879788	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3762339	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3762340	0.95[JPT][hapmap]
rs3790613	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3790614	0.83[ASN][1000 genomes]
rs3811453	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs3811455	0.91[JPT][hapmap]
rs3828077	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs3935419	0.91[JPT][hapmap]
rs4240871	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4620534	0.91[JPT][hapmap]
rs60633748	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6427509	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6657214	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6673752	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6719	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7517578	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7524346	0.82[ASN][1000 genomes]
rs9700528	0.82[EUR][1000 genomes]
rs9803857	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9943093	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
7	esv3453084	chr1:154156328-154161626	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
8	esv3453085	chr1:154156328-154161626	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11265251	HAX1	cis	lymphoblastoid	seeQTL
rs11265251	SCARNA4	cis	cerebellum	SCAN
rs11265251	C1orf43	cis	parietal	SCAN
rs11265251	SPRR2D	cis	parietal	SCAN
rs11265251	CRTC2	cis	cerebellum	SCAN
rs11265251	UBAP2L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154154000-154157400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:154156200-154157200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:154156200-154158400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:154156200-154158400	Weak transcription	Fetal Intestine Small	intestine
5	chr1:154156200-154158600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:154156200-154158800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:154156200-154163000	Weak transcription	Psoas Muscle	Psoas
8	chr1:154156400-154157200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:154156400-154157200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:154156400-154157200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:154156400-154157200	Enhancers	HMEC	breast
12	chr1:154156400-154158200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:154156400-154158200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:154156400-154158200	Weak transcription	HSMMtube	muscle
15	chr1:154156400-154158400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:154156400-154158400	Weak transcription	Stomach Mucosa	stomach
17	chr1:154156400-154158400	Weak transcription	HSMM	muscle
18	chr1:154156400-154158600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:154156400-154158600	Weak transcription	Fetal Kidney	kidney
20	chr1:154156400-154158600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:154156400-154158800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:154156400-154158800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:154156400-154158800	Weak transcription	Fetal Intestine Large	intestine
24	chr1:154156400-154159000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:154156400-154159000	Weak transcription	A549	lung
26	chr1:154156400-154159400	Weak transcription	Small Intestine	intestine
27	chr1:154156400-154159600	Weak transcription	GM12878-XiMat	blood
28	chr1:154156400-154163200	Weak transcription	Fetal Muscle Leg	muscle
29	chr1:154156400-154164200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr1:154156600-154157200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:154156600-154157400	Enhancers	K562	blood
32	chr1:154156600-154157600	Enhancers	Hela-S3	cervix
33	chr1:154156600-154158200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:154156600-154158200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:154156600-154158200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:154156600-154158200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:154156600-154158200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr1:154156600-154158400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:154156600-154158400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:154156600-154158400	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:154156600-154158400	Weak transcription	HepG2	liver
42	chr1:154156600-154158600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:154156600-154158800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:154156600-154158800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:154156600-154158800	Weak transcription	Pancreas	Pancrea
46	chr1:154156600-154164200	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:154156800-154164200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:154157000-154157400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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