Variant report

Variant	rs1647403
Chromosome Location	chr11:57426428-57426429
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57335100..57336885-chr11:57425174..57426738,2	K562	blood:
2	chr11:57423095..57430151-chr11:57432283..57438412,24	K562	blood:
3	chr11:57423375..57427275-chr11:57433374..57437610,8	MCF-7	breast:
4	chr11:57423749..57426682-chr11:57508630..57510179,2	K562	blood:
5	chr11:57414343..57418921-chr11:57423216..57427343,7	K562	blood:
6	chr11:57417074..57418991-chr11:57424889..57426673,2	K562	blood:
7	chr11:57424563..57426708-chr11:57434107..57436084,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156599	Chromatin interaction
ENSG00000254732	Chromatin interaction
ENSG00000211450	Chromatin interaction
ENSG00000172409	Chromatin interaction
ENSG00000156587	Chromatin interaction
ENSG00000166793	Chromatin interaction
ENSG00000254602	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10750870	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs10792110	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs10896644	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs10896649	0.88[JPT][hapmap]
rs10896653	0.82[ASN][1000 genomes]
rs11229109	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs11570176	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs11570181	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs12270209	0.84[ASN][1000 genomes]
rs12274865	0.84[ASN][1000 genomes]
rs12363024	0.85[ASN][1000 genomes]
rs12805343	0.82[ASN][1000 genomes]
rs1424753	0.85[ASN][1000 genomes]
rs1613592	0.82[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1624389	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1631684	0.88[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1647394	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17455422	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs17455626	0.85[ASN][1000 genomes]
rs1783818	0.84[ASN][1000 genomes]
rs1783824	0.82[ASN][1000 genomes]
rs1783826	0.88[JPT][hapmap]
rs1783827	0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1783828	0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1783829	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1783976	0.85[ASN][1000 genomes]
rs1783978	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs1783979	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs1783980	0.88[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1783981	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs1783983	0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1783984	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1783985	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1785498	0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1785499	0.82[ASN][1000 genomes]
rs1798172	0.82[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1798173	0.82[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1798177	0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2156638	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs2956981	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2956982	0.82[ASN][1000 genomes]
rs3017889	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs36036499	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4611222	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs56392705	0.82[ASN][1000 genomes]
rs627145	0.88[JPT][hapmap]
rs644219	0.82[ASN][1000 genomes]
rs645145	0.82[ASN][1000 genomes]
rs652191	0.82[ASN][1000 genomes]
rs653889	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs659165	0.82[ASN][1000 genomes]
rs665058	0.86[JPT][hapmap]
rs671508	0.82[ASN][1000 genomes]
rs682258	0.82[ASN][1000 genomes]
rs686489	0.83[ASN][1000 genomes]
rs7105506	0.85[ASN][1000 genomes]
rs7115528	0.85[ASN][1000 genomes]
rs7117020	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs7120868	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7479922	0.85[ASN][1000 genomes]
rs7947357	0.88[JPT][hapmap];0.84[EUR][1000 genomes]
rs929934	0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers 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	93 gene(s)	inside rSNPs	diseases
6	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1647403	YPEL4	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57425600-57427000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:57425800-57426800	Weak transcription	Placenta	Placenta
3	chr11:57425800-57427000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:57425800-57427000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr11:57425800-57427000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:57425800-57427000	Weak transcription	Aorta	Aorta
7	chr11:57425800-57427000	Weak transcription	Esophagus	oesophagus
8	chr11:57425800-57427000	Weak transcription	Gastric	stomach
9	chr11:57425800-57427000	Weak transcription	Left Ventricle	heart
10	chr11:57425800-57427000	Weak transcription	Lung	lung
11	chr11:57425800-57427000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr11:57425800-57427000	Weak transcription	Small Intestine	intestine
13	chr11:57425800-57427000	Weak transcription	Spleen	Spleen
14	chr11:57426000-57426600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr11:57426000-57426600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr11:57426000-57426600	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr11:57426000-57426600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr11:57426000-57426600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:57426000-57426600	Enhancers	Brain Cingulate Gyrus	brain
20	chr11:57426000-57426600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr11:57426000-57426600	Enhancers	Duodenum Mucosa	Duodenum
22	chr11:57426000-57426600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr11:57426000-57426800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr11:57426000-57426800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr11:57426000-57426800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr11:57426000-57426800	Enhancers	Primary B cells from cord blood	blood
27	chr11:57426000-57426800	Enhancers	Primary T cells from cord blood	blood
28	chr11:57426000-57426800	Enhancers	Primary T cells fromperipheralblood	blood
29	chr11:57426000-57426800	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr11:57426000-57426800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr11:57426000-57426800	Enhancers	Liver	Liver
32	chr11:57426000-57426800	Weak transcription	Fetal Intestine Large	intestine
33	chr11:57426000-57426800	Weak transcription	HSMM	muscle
34	chr11:57426000-57426800	Weak transcription	K562	blood
35	chr11:57426000-57427000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr11:57426000-57427000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:57426000-57427000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr11:57426000-57427000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr11:57426000-57427000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr11:57426000-57427000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr11:57426000-57427000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr11:57426000-57427000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr11:57426000-57427000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr11:57426000-57427000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr11:57426000-57427000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr11:57426000-57427000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr11:57426000-57427000	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr11:57426000-57427000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr11:57426000-57427000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr11:57426000-57427000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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