Variant report

Variant	rs1002285
Chromosome Location	chr4:57772712-57772713
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	TCF7L2	chr4:57772610-57772979	HEK293	kidney:	n/a	n/a
2	SPI1	chr4:57772660-57772988	HL-60	blood:	n/a	n/a
3	SPI1	chr4:57772594-57773032	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:57766086..57769107-chr4:57769697..57772712,3	K562	blood:
2	chr4:57771688..57776264-chr4:57841866..57845328,7	MCF-7	breast:
3	chr4:57771524..57779492-chr4:57841270..57849741,26	K562	blood:

Variant related genes	Relation type
REST	TF binding region
ENSG00000084092	Chromatin interaction
ENSG00000047315	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10020462	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10023088	0.82[JPT][hapmap]
rs1056364	0.82[JPT][hapmap]
rs11573125	0.80[GIH][hapmap]
rs12650737	0.80[JPT][hapmap]
rs13121027	0.81[ASN][1000 genomes]
rs17087265	0.87[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs1708762	0.87[EUR][1000 genomes]
rs1708764	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1713985	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806746	0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3821994	0.81[GIH][hapmap]
rs4280804	0.91[EUR][1000 genomes]
rs4865163	0.86[EUR][1000 genomes]
rs4865164	0.90[EUR][1000 genomes]
rs61598699	0.86[ASN][1000 genomes]
rs6554400	0.87[ASN][1000 genomes]
rs73165993	0.80[ASN][1000 genomes]
rs781546	0.86[EUR][1000 genomes]
rs781547	0.86[EUR][1000 genomes]
rs781548	0.83[EUR][1000 genomes]
rs781550	0.85[EUR][1000 genomes]
rs781655	0.87[EUR][1000 genomes]
rs781661	0.94[ASN][1000 genomes]
rs796680	0.85[EUR][1000 genomes]
rs796681	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs802920	0.89[AFR][1000 genomes];0.97[EUR][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	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
4	nsv822562	chr4:57768655-57779715	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv12676	chr4:57772270-57775584	Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1002285	KDR	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57761600-57773000	Weak transcription	Right Atrium	heart
2	chr4:57771800-57773200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:57772000-57772800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:57772000-57772800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
5	chr4:57772000-57773000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
6	chr4:57772000-57773400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr4:57772200-57773000	Enhancers	Primary T cells from cord blood	blood
8	chr4:57772200-57773200	Enhancers	Primary B cells from cord blood	blood
9	chr4:57772400-57772800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
10	chr4:57772600-57772800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
11	chr4:57772600-57772800	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
12	chr4:57772600-57772800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:57772600-57772800	Enhancers	Fetal Kidney	kidney
14	chr4:57772600-57772800	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr4:57772600-57773000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:57772600-57773000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:57772600-57773000	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr4:57772600-57773000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr4:57772600-57773000	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr4:57772600-57773000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr4:57772600-57773000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr4:57772600-57773200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
23	chr4:57772600-57773200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
24	chr4:57772600-57773200	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr4:57772600-57773200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr4:57772600-57773200	Enhancers	Adipose Nuclei	Adipose
27	chr4:57772600-57773200	Enhancers	Brain Hippocampus Middle	brain
28	chr4:57772600-57773200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr4:57772600-57773200	Enhancers	Fetal Thymus	thymus
30	chr4:57772600-57773200	Enhancers	Stomach Mucosa	stomach
31	chr4:57772600-57773200	Enhancers	Dnd41	blood
32	chr4:57772600-57773200	Bivalent Enhancer	K562	blood
33	chr4:57772600-57773400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
34	chr4:57772600-57773600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell

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