Variant report

Variant	rs9306995
Chromosome Location	chr4:76577044-76577045
allele	A/G
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	GATA3	chr4:76576966-76577803	MCF-7	breast:	n/a	chr4:76577463-76577479 chr4:76577466-76577476 chr4:76577466-76577475 chr4:76577468-76577475 chr4:76577468-76577475 chr4:76577467-76577475 chr4:76577468-76577475 chr4:76577461-76577482
2	POLR2A	chr4:76576258-76577612	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:76572563..76577476-chr4:76578400..76583140,7	K562	blood:
2	chr4:76576940..76580449-chr4:76596844..76600362,4	MCF-7	breast:
3	chr4:76573131..76578046-chr4:76580054..76584668,6	K562	blood:
4	chr4:76575878..76577705-chr4:76597266..76598785,2	MCF-7	breast:
5	chr4:76575310..76582874-chr4:76594032..76598652,8	K562	blood:
6	chr4:76568880..76572103-chr4:76574675..76578166,4	K562	blood:
7	chr4:76575506..76578468-chr4:76770062..76772274,2	MCF-7	breast:
8	chr4:76576972..76578764-chr4:76649113..76651265,2	MCF-7	breast:

Variant related genes	Relation type
G3BP2	TF binding region
ENSG00000138757	Chromatin interaction
ENSG00000138768	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10004891	0.90[AMR][1000 genomes]
rs10020040	0.83[ASN][1000 genomes]
rs10856855	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10856857	0.84[AMR][1000 genomes]
rs11097050	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729983	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11731107	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11731569	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12233785	0.86[AMR][1000 genomes]
rs12647909	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13103092	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13124724	0.83[JPT][hapmap];0.80[AMR][1000 genomes]
rs13134512	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13135568	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13148199	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13152407	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17280938	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2055998	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2137429	1.00[ASW][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28693963	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28709419	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35443067	0.82[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs3796479	0.92[CHD][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs4859538	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4859541	0.83[EUR][1000 genomes]
rs4859966	0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs6818949	0.82[AMR][1000 genomes]
rs7665811	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9306994	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9994998	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879495	chr4:76493256-76585823	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv879496	chr4:76493256-76620803	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv879497	chr4:76519096-76620803	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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
4	esv1793652	chr4:76521217-76581775	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9306995	FAM47E	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76556200-76590000	Weak transcription	Small Intestine	intestine
2	chr4:76565000-76584200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:76565600-76588600	Strong transcription	Fetal Thymus	thymus
4	chr4:76565600-76588800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:76566200-76596600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:76566400-76593800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:76566800-76585800	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:76567000-76588200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr4:76567000-76588200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr4:76567200-76579000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr4:76567200-76585800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:76567200-76586200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:76567400-76587400	Strong transcription	Placenta	Placenta
14	chr4:76567400-76588400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr4:76567400-76588400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr4:76567400-76596600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:76567600-76587000	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr4:76567600-76587200	Strong transcription	Liver	Liver
19	chr4:76567600-76588000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr4:76567600-76588200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr4:76567600-76588400	Strong transcription	Dnd41	blood
22	chr4:76568000-76583600	Strong transcription	Duodenum Mucosa	Duodenum
23	chr4:76568000-76587400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:76568000-76588600	Strong transcription	Primary B cells from cord blood	blood
25	chr4:76568200-76578000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:76568200-76584800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:76568600-76583600	Strong transcription	Adipose Nuclei	Adipose
28	chr4:76568600-76588600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr4:76568800-76577400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:76568800-76578600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:76568800-76579000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr4:76568800-76581200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr4:76568800-76583400	Strong transcription	Fetal Intestine Large	intestine
34	chr4:76568800-76584000	Strong transcription	NH-A	brain
35	chr4:76568800-76587800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:76569200-76580400	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr4:76569400-76584000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr4:76569600-76584000	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr4:76569600-76585000	Weak transcription	Stomach Mucosa	stomach
40	chr4:76569600-76586800	Strong transcription	Primary hematopoietic stem cells	blood
41	chr4:76569800-76577800	Strong transcription	HepG2	liver
42	chr4:76569800-76578600	Strong transcription	A549	lung
43	chr4:76569800-76579600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr4:76569800-76588600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr4:76570000-76578000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:76570000-76579200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:76570000-76587200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr4:76570000-76588200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:76570200-76578000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr4:76570600-76587200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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