Variant report

Variant	rs6533842
Chromosome Location	chr4:79564395-79564396
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr4:79563980-79564549	ECC-1	luminal epithelium:	n/a	n/a
2	SPI1	chr4:79564203-79564622	HL-60	blood:	n/a	n/a
3	RUNX3	chr4:79564032-79564520	GM12878	blood:	n/a	n/a
4	TEAD4	chr4:79563928-79564454	K562	blood:	n/a	n/a
5	SPI1	chr4:79564242-79564454	GM12891	blood:	n/a	n/a
6	RCOR1	chr4:79563983-79564434	K562	blood:	n/a	n/a
7	SPI1	chr4:79564188-79564479	GM12878	blood:	n/a	n/a
8	SPI1	chr4:79564294-79564422	GM12878	blood:	n/a	n/a
9	EBF1	chr4:79564319-79564454	GM12878	blood:	n/a	n/a
10	ZKSCAN1	chr4:79564145-79564453	Hela-S3	cervix:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:79555903..79561750-chr4:79563110..79566277,7	K562	blood:
2	chr4:79563120..79566472-chr4:79698388..79700680,4	K562	blood:
3	chr4:79557761..79562686-chr4:79563110..79568703,4	K562	blood:
4	chr4:79549184..79553600-chr4:79560172..79565329,6	K562	blood:
5	chr4:79564124..79566354-chr4:79779216..79781048,2	MCF-7	breast:
6	chr4:79563690..79568625-chr4:79568843..79572048,4	K562	blood:
7	chr4:79562196..79569044-chr4:79695847..79699797,11	MCF-7	breast:
8	chr4:79563449..79567560-chr4:79569303..79574487,6	K562	blood:
9	chr4:79562740..79566241-chr4:79702324..79704926,3	MCF-7	breast:
10	chr4:79564080..79567985-chr4:79696414..79698633,7	MCF-7	breast:

No data

Variant related genes	Relation type
LINC01094	TF binding region
ENSG00000238816	Chromatin interaction
ENSG00000251019	Chromatin interaction
ENSG00000260278	Chromatin interaction
ENSG00000200998	Chromatin interaction
ENSG00000138756	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10001246	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs10007186	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs10019240	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10212636	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1107606	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1108907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11724268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11724602	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11727844	0.89[YRI][hapmap]
rs11728013	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11731482	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11733032	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11733269	0.90[CEU][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs11736376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11942573	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12233694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12233707	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12643488	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12646646	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650411	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12711032	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13120630	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13138005	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs1972024	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28597797	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34325799	0.86[EUR][1000 genomes]
rs4073678	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4073679	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4074673	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4074674	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4075927	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4077709	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4270605	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4306980	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4353930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4632683	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4643844	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4975148	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6533821	0.90[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs6533825	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6533835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533845	0.85[AMR][1000 genomes]
rs6533847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6811335	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6811782	0.88[JPT][hapmap]
rs6812227	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6812441	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6814739	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6819484	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6824014	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6829061	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6829198	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6834587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6835998	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6836513	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6838443	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6840592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6841654	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6845893	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6846346	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6851341	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6854055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6858740	0.88[JPT][hapmap]
rs7317	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7657082	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7661370	0.89[YRI][hapmap]
rs7669674	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7669866	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7670506	0.90[EUR][1000 genomes]
rs7671564	0.89[YRI][hapmap]
rs7680749	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7680766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7682984	0.84[EUR][1000 genomes]
rs7686273	0.88[YRI][hapmap]
rs7689154	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7697461	0.88[EUR][1000 genomes]
rs9998136	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6533842	PRDM8	cis	parietal	SCAN
rs6533842	ART3	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79551400-79578200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:79555800-79566400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:79557200-79568000	Enhancers	Primary B cells from cord blood	blood
4	chr4:79560200-79565200	Weak transcription	Primary T cells from cord blood	blood
5	chr4:79560200-79565400	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr4:79560200-79565600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:79561000-79565400	Weak transcription	NHEK	skin
8	chr4:79561600-79565000	Enhancers	Placenta	Placenta
9	chr4:79561600-79568000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:79561800-79566800	Enhancers	K562	blood
11	chr4:79562000-79568000	Enhancers	Primary B cells from peripheral blood	blood
12	chr4:79562400-79566400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:79562800-79567600	Enhancers	Primary hematopoietic stem cells	blood
14	chr4:79563000-79565000	Enhancers	Placenta Amnion	Placenta Amnion
15	chr4:79563000-79566000	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr4:79563200-79564400	Enhancers	Fetal Thymus	thymus
17	chr4:79563200-79568800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr4:79563400-79564800	Flanking Active TSS	GM12878-XiMat	blood
19	chr4:79563400-79565000	Enhancers	Brain Anterior Caudate	brain
20	chr4:79563400-79567200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:79563600-79564400	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr4:79563600-79564800	Enhancers	HSMMtube	muscle
23	chr4:79563600-79565000	Enhancers	Brain Substantia Nigra	brain
24	chr4:79563800-79566600	Enhancers	Hela-S3	cervix
25	chr4:79564000-79564400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:79564000-79564400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:79564000-79564400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:79564000-79564400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr4:79564000-79564400	Enhancers	Brain Cingulate Gyrus	brain
30	chr4:79564000-79564400	Enhancers	Fetal Heart	heart
31	chr4:79564000-79564400	Enhancers	Spleen	Spleen
32	chr4:79564000-79564400	Enhancers	HMEC	breast
33	chr4:79564000-79564400	Enhancers	HSMM	muscle
34	chr4:79564000-79564600	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr4:79564000-79564600	Enhancers	Adipose Nuclei	Adipose
36	chr4:79564000-79564600	Enhancers	Duodenum Mucosa	Duodenum
37	chr4:79564000-79564600	Enhancers	Stomach Mucosa	stomach
38	chr4:79564000-79564800	Enhancers	Brain Hippocampus Middle	brain
39	chr4:79564000-79564800	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr4:79564000-79564800	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr4:79564000-79568000	Enhancers	Fetal Intestine Large	intestine
42	chr4:79564200-79564400	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr4:79564200-79564400	Enhancers	Esophagus	oesophagus
44	chr4:79564200-79564400	Enhancers	Left Ventricle	heart
45	chr4:79564200-79564400	Enhancers	Lung	lung
46	chr4:79564200-79564400	Enhancers	HUVEC	blood vessel
47	chr4:79564200-79564600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:79564200-79564600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr4:79564200-79564600	Enhancers	Colon Smooth Muscle	Colon
50	chr4:79564200-79564600	Enhancers	NHDF-Ad	bronchial

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