Variant report

Variant	rs17003396
Chromosome Location	chr4:79538143-79538144
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79536352..79538431-chr4:79574021..79576567,2	K562	blood:
2	chr4:79534997..79539335-chr4:79548255..79551176,6	K562	blood:
3	chr4:79503826..79506330-chr4:79536757..79539356,2	K562	blood:
4	chr4:79534010..79538453-chr4:79546769..79551125,4	K562	blood:
5	chr4:79517752..79520186-chr4:79537691..79539764,2	K562	blood:

Variant related genes	Relation type
ENSG00000138772	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1042515	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725235	0.83[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs11727844	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11728517	0.86[ASN][1000 genomes]
rs12640075	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35628566	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4382063	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap]
rs56023152	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57415147	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57896096	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58089913	0.84[ASN][1000 genomes]
rs59133103	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5942	0.83[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs5950	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67280698	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817792	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6819559	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6836185	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6837823	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72607862	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72607863	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72607864	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72607865	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72607866	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7661370	1.00[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.91[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7668240	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7671564	0.89[YRI][hapmap]
rs7672903	0.83[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs7686273	0.87[CHB][hapmap];0.80[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7694152	0.83[CHB][hapmap];0.84[JPT][hapmap];0.84[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17003396	ART3	cis	parietal	SCAN
rs17003396	RP11-792D21.2	cis	Whole Blood	GTEx
rs17003396	ANXA3	cis	multi-tissue	Pritchard
rs17003396	SCARB2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79491800-79542600	Weak transcription	NH-A	brain
2	chr4:79518000-79548000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:79518600-79543600	Weak transcription	Stomach Mucosa	stomach
4	chr4:79524200-79543400	Weak transcription	A549	lung
5	chr4:79527800-79542600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:79527800-79542600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:79530000-79540000	Enhancers	Primary T cells from cord blood	blood
8	chr4:79531400-79543000	Weak transcription	Hela-S3	cervix
9	chr4:79531800-79543200	Weak transcription	HUVEC	blood vessel
10	chr4:79533800-79538600	Enhancers	Fetal Intestine Large	intestine
11	chr4:79533800-79541000	Enhancers	Fetal Intestine Small	intestine
12	chr4:79533800-79548800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:79534600-79547800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:79534800-79538200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:79535400-79542600	Weak transcription	Placenta	Placenta
16	chr4:79535600-79539200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:79535600-79543000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:79536200-79538200	Enhancers	Placenta Amnion	Placenta Amnion
19	chr4:79536200-79538600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr4:79536200-79538600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:79536400-79538600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:79536400-79550600	Weak transcription	Left Ventricle	heart
23	chr4:79536600-79538600	Weak transcription	Primary B cells from cord blood	blood
24	chr4:79536800-79538400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:79536800-79538600	Weak transcription	Fetal Thymus	thymus
26	chr4:79536800-79539200	Weak transcription	GM12878-XiMat	blood
27	chr4:79536800-79542600	Weak transcription	Right Atrium	heart
28	chr4:79537000-79538800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr4:79537000-79545800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr4:79537600-79538600	Weak transcription	Dnd41	blood
31	chr4:79537800-79539000	Weak transcription	NHDF-Ad	bronchial
32	chr4:79537800-79542600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:79537800-79543400	Weak transcription	HSMM	muscle
34	chr4:79538000-79538400	Weak transcription	K562	blood

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