Variant report

Variant	rs2282683
Chromosome Location	chr9:79117751-79117752
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79074775..79077434-chr9:79117333..79119392,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10119532	0.84[MEX][hapmap]
rs1057406	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144926	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11144931	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11144933	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12375958	0.82[ASN][1000 genomes]
rs12553343	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs2093839	0.92[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2147266	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3808903	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4745552	0.90[MEX][hapmap]
rs589561	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap]
rs590666	0.80[JPT][hapmap];0.80[YRI][hapmap]
rs619429	0.80[JPT][hapmap];0.80[YRI][hapmap]
rs620295	0.80[JPT][hapmap];0.80[YRI][hapmap]
rs634064	0.80[JPT][hapmap]
rs707739	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7871849	0.90[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949417	chr9:79078703-79282589	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv893480	chr9:79115844-79222584	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv437089	chr9:79116975-79139590	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2282683	ZFAND5	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79075600-79117800	Weak transcription	Primary T cells from cord blood	blood
2	chr9:79093400-79142800	Weak transcription	Fetal Stomach	stomach
3	chr9:79093800-79118000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr9:79094200-79120200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:79103800-79117800	Weak transcription	Thymus	Thymus
6	chr9:79108200-79117800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:79112000-79117800	Weak transcription	Fetal Intestine Small	intestine
8	chr9:79112000-79120400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:79114400-79120200	Weak transcription	Pancreas	Pancrea
10	chr9:79114400-79122800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr9:79115000-79122600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:79115200-79119200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr9:79115200-79119800	Strong transcription	Primary B cells from cord blood	blood
14	chr9:79115200-79120400	Strong transcription	Fetal Intestine Large	intestine
15	chr9:79115400-79117800	Weak transcription	NH-A	brain
16	chr9:79115400-79120400	Strong transcription	Duodenum Mucosa	Duodenum
17	chr9:79115600-79118000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr9:79115600-79120800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:79115800-79118200	Genic enhancers	HSMM	muscle
20	chr9:79115800-79118400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:79115800-79118600	Genic enhancers	Osteobl	bone
22	chr9:79115800-79118800	Genic enhancers	Muscle Satellite Cultured Cells	--
23	chr9:79116000-79117800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:79116000-79117800	Weak transcription	Spleen	Spleen
25	chr9:79116000-79119400	Weak transcription	Left Ventricle	heart
26	chr9:79116200-79118000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr9:79116200-79118000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr9:79116200-79118800	Strong transcription	Primary B cells from peripheral blood	blood
29	chr9:79116200-79119800	Strong transcription	Primary hematopoietic stem cells	blood
30	chr9:79116400-79118800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr9:79116400-79118800	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr9:79116400-79119000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr9:79116400-79119600	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr9:79116400-79119800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:79116400-79119800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr9:79116600-79118200	Weak transcription	Fetal Muscle Leg	muscle
37	chr9:79116600-79118800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr9:79116600-79118800	Strong transcription	NHDF-Ad	bronchial
39	chr9:79116600-79119000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr9:79116600-79119000	Strong transcription	GM12878-XiMat	blood
41	chr9:79116600-79119200	Weak transcription	Liver	Liver
42	chr9:79116600-79121200	Weak transcription	Esophagus	oesophagus
43	chr9:79116800-79118400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:79116800-79119400	Weak transcription	Fetal Brain Female	brain
45	chr9:79116800-79120000	Weak transcription	Adipose Nuclei	Adipose
46	chr9:79116800-79120200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr9:79117000-79119200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr9:79117000-79120000	Weak transcription	Aorta	Aorta
49	chr9:79117000-79120000	Strong transcription	HMEC	breast
50	chr9:79117200-79118000	Strong transcription	HSMMtube	muscle

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