Variant report

Variant	rs9859785
Chromosome Location	chr3:105279634-105279635
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105272104..105273978-chr3:105278309..105280782,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1044243	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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1157	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs13315085	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13315918	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13317140	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13317379	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs13320956	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322383	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13325976	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[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17181561	0.84[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs17181701	0.84[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs17189101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17189643	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17189711	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291374	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28452673	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3772552	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772556	0.88[CHD][hapmap]
rs72989914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72989943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73006164	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs751554	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[AMR][1000 genomes]
rs7610031	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[MEX][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]
rs7619149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633779	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645474	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][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]
rs9288807	0.84[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9288811	0.96[ASN][1000 genomes]
rs9828587	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829190	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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9831077	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9832489	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9839346	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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840990	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9841699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842772	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9842815	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9843750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9847971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851399	0.92[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9855810	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[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862725	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873424	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876895	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[MEX][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]
rs9876906	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[AMR][1000 genomes]
rs9878315	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882494	0.84[CEU][hapmap]
rs9990253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv829651	chr3:105203424-105402136	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv460811	chr3:105212993-105316769	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv591240	chr3:105212993-105316769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	esv3357241	chr3:105277162-105281660	Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9859785	DZIP3	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105221400-105300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:105242000-105293600	Weak transcription	Lung	lung
3	chr3:105242400-105280400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:105246600-105284400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:105248000-105281200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:105248400-105291200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:105249800-105284000	Weak transcription	Fetal Stomach	stomach
8	chr3:105249800-105285200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:105254800-105279800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:105259400-105281200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr3:105260800-105297000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:105260800-105299800	Weak transcription	Pancreas	Pancrea
13	chr3:105263000-105295400	Weak transcription	Brain Angular Gyrus	brain
14	chr3:105267600-105293800	Weak transcription	Brain Anterior Caudate	brain
15	chr3:105268400-105297800	Weak transcription	NHLF	lung
16	chr3:105271600-105280600	Weak transcription	Fetal Intestine Large	intestine
17	chr3:105271600-105282600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr3:105271600-105297000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:105271600-105303000	Weak transcription	Aorta	Aorta
20	chr3:105271800-105285800	Weak transcription	HUVEC	blood vessel
21	chr3:105272000-105291200	Weak transcription	Brain Substantia Nigra	brain
22	chr3:105272200-105312800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:105272400-105302800	Weak transcription	NHEK	skin
24	chr3:105273000-105295200	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:105273200-105292200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:105273200-105294000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:105273200-105295800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr3:105273200-105303000	Weak transcription	HMEC	breast
29	chr3:105273400-105280800	Weak transcription	A549	lung
30	chr3:105273400-105285600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:105273400-105287800	Weak transcription	Primary B cells from peripheral blood	blood
32	chr3:105273400-105292800	Weak transcription	Ovary	ovary
33	chr3:105273400-105297600	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr3:105273400-105297600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr3:105273400-105299800	Weak transcription	NHDF-Ad	bronchial
36	chr3:105273600-105280800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:105273600-105283200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:105273800-105291000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:105273800-105297400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr3:105274000-105291200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:105274000-105303000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:105274600-105293400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr3:105277200-105299200	Weak transcription	Brain Hippocampus Middle	brain
44	chr3:105277400-105284400	Weak transcription	NH-A	brain
45	chr3:105277600-105281200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:105278600-105287200	Weak transcription	HSMM	muscle
47	chr3:105278600-105289800	Weak transcription	Primary B cells from cord blood	blood
48	chr3:105278600-105290800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:105278600-105297000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr3:105278600-105297400	Weak transcription	GM12878-XiMat	blood

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