Variant report

Variant	rs4339543
Chromosome Location	chr7:47816403-47816404
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:47814103..47816415-chr7:47816480..47819252,2	K562	blood:
2	chr7:47624955..47626619-chr7:47816230..47818018,2	MCF-7	breast:
3	chr7:47789337..47791664-chr7:47815360..47817822,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12536897	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs1597936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869321	0.85[ASN][1000 genomes]
rs2348461	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2881920	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4295569	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs4481491	0.86[ASN][1000 genomes]
rs6953528	0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[ASN][1000 genomes]
rs6961895	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs718076	0.85[CHB][hapmap]
rs718077	0.85[CHB][hapmap]
rs7797545	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv888003	chr7:47694270-47907214	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1018608	chr7:47708525-47831535	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1022906	chr7:47709936-47831535	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1015163	chr7:47734913-47832389	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv538831	chr7:47734913-47832389	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv830990	chr7:47767540-47837584	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4339543	IKZF1	cis	parietal	SCAN
rs4339543	GRB10	cis	parietal	SCAN
rs4339543	HUS1	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47812800-47817400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:47813000-47817400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr7:47813000-47817400	Weak transcription	Fetal Intestine Large	intestine
4	chr7:47813400-47817400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr7:47814400-47823200	Enhancers	HepG2	liver
6	chr7:47814800-47817600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr7:47815000-47817400	Weak transcription	NH-A	brain
8	chr7:47815000-47818600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr7:47815000-47821600	Weak transcription	Aorta	Aorta
10	chr7:47815800-47816600	Enhancers	HMEC	breast
11	chr7:47815800-47818800	Weak transcription	Osteobl	bone
12	chr7:47815800-47821600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:47815800-47821600	Weak transcription	NHLF	lung
14	chr7:47816200-47817400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr7:47816200-47817400	Weak transcription	Liver	Liver
16	chr7:47816200-47818400	Weak transcription	HSMMtube	muscle
17	chr7:47816200-47818600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr7:47816200-47826000	Weak transcription	Right Atrium	heart
19	chr7:47816400-47816800	Weak transcription	A549	lung
20	chr7:47816400-47817200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr7:47816400-47817400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr7:47816400-47817400	Weak transcription	NHEK	skin
23	chr7:47816400-47821400	Weak transcription	Muscle Satellite Cultured Cells	--

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