Variant report

Variant	rs1277287
Chromosome Location	chr4:57853147-57853148
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	chr4:57841254..57846591-chr4:57852896..57857451,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000047315	Chromatin interaction
ENSG00000084092	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10866440	1.00[JPT][hapmap]
rs10866441	1.00[JPT][hapmap]
rs1105434	1.00[JPT][hapmap]
rs1107675	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11727683	0.84[ASN][1000 genomes]
rs11730321	0.93[JPT][hapmap]
rs11735158	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11932673	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12500454	1.00[JPT][hapmap]
rs1277271	0.89[ASN][1000 genomes]
rs1277288	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13108245	1.00[JPT][hapmap]
rs13121176	0.80[ASN][1000 genomes]
rs1315005	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1315006	0.84[EUR][1000 genomes]
rs1625691	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17081937	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17087307	0.82[ASN][1000 genomes]
rs17087317	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17087411	0.87[JPT][hapmap]
rs17087414	0.87[JPT][hapmap]
rs1713994	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1713997	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1713998	1.00[ASW][hapmap]
rs1718837	0.91[CEU][hapmap];0.95[TSI][hapmap]
rs1718839	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1718882	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1718886	0.81[TSI][hapmap]
rs1877669	1.00[JPT][hapmap]
rs1976780	0.82[ASN][1000 genomes]
rs2228991	1.00[JPT][hapmap]
rs3000	1.00[JPT][hapmap]
rs34576794	0.87[ASN][1000 genomes]
rs34659774	0.82[ASN][1000 genomes]
rs3733306	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs3796528	1.00[JPT][hapmap]
rs3806745	1.00[JPT][hapmap]
rs41552420	0.82[ASN][1000 genomes]
rs41556916	0.84[ASN][1000 genomes]
rs56182208	0.84[ASN][1000 genomes]
rs56285301	0.84[ASN][1000 genomes]
rs57469512	0.84[ASN][1000 genomes]
rs6554398	1.00[JPT][hapmap]
rs6816457	0.89[ASN][1000 genomes]
rs6838948	1.00[JPT][hapmap]
rs6847086	0.82[JPT][hapmap]
rs6852110	1.00[JPT][hapmap]
rs708547	0.86[TSI][hapmap]
rs73242624	0.86[EUR][1000 genomes]
rs73242631	0.82[ASN][1000 genomes]
rs7661194	1.00[JPT][hapmap]
rs7680734	1.00[JPT][hapmap]
rs781665	0.88[ASN][1000 genomes]
rs781666	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs781668	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9942208	1.00[JPT][hapmap];0.82[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	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1277287	IGFBP7	cis	multi-tissue	Pritchard
rs1277287	POLR2B	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57846000-57853600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:57846000-57855600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:57846000-57881000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:57846200-57853600	Weak transcription	Esophagus	oesophagus
5	chr4:57846200-57861600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:57846200-57861800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:57846600-57853200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr4:57846600-57861200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr4:57846800-57900000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:57847000-57853800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:57847000-57853800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr4:57847000-57861600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:57847200-57853400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:57847200-57853600	Weak transcription	Spleen	Spleen
15	chr4:57847600-57853800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:57847600-57856000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr4:57847800-57853600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr4:57848000-57861400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr4:57848400-57860800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr4:57848400-57875200	Weak transcription	Stomach Mucosa	stomach
21	chr4:57848600-57900000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr4:57849000-57855200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:57849000-57900000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:57849200-57869000	Strong transcription	Primary B cells from peripheral blood	blood
25	chr4:57849200-57886200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:57849400-57853800	Weak transcription	Right Ventricle	heart
27	chr4:57849400-57854000	Weak transcription	Small Intestine	intestine
28	chr4:57849400-57857600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:57849600-57884600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr4:57849800-57857000	Strong transcription	Fetal Intestine Small	intestine
31	chr4:57849800-57861400	Weak transcription	Psoas Muscle	Psoas
32	chr4:57850000-57854200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:57850000-57855800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:57850200-57854800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:57850400-57856000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr4:57850400-57858200	Strong transcription	Primary B cells from cord blood	blood
37	chr4:57850400-57858600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:57850600-57854400	Strong transcription	K562	blood
39	chr4:57850600-57855400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:57850600-57855600	Strong transcription	NH-A	brain
41	chr4:57850600-57870200	Strong transcription	GM12878-XiMat	blood
42	chr4:57850600-57899400	Strong transcription	Fetal Thymus	thymus
43	chr4:57850800-57859400	Strong transcription	Fetal Stomach	stomach
44	chr4:57850800-57899400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr4:57851000-57860600	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr4:57851000-57861200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:57851000-57899200	Strong transcription	Primary T cells from cord blood	blood
48	chr4:57851000-57899400	Strong transcription	Duodenum Mucosa	Duodenum
49	chr4:57851200-57854600	Strong transcription	Fetal Lung	lung
50	chr4:57851200-57858400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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