Variant report

Variant	rs1317244
Chromosome Location	chr3:112053565-112053566
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	chr3:112052345..112054034-chr3:112155349..112157049,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2399415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2399419	0.81[CEU][hapmap]
rs2399422	0.81[CEU][hapmap]
rs59495246	0.90[ASN][1000 genomes]
rs61651681	0.90[ASN][1000 genomes]
rs73856005	0.92[ASN][1000 genomes]
rs7612748	0.81[CEU][hapmap]
rs7637088	0.81[CEU][hapmap]
rs9818407	0.81[CEU][hapmap]
rs9838489	0.82[CEU][hapmap]
rs9842650	0.96[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs9881834	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]

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	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1317244	ZNF80	cis	cerebellum	SCAN
rs1317244	ATP6V1A	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112050600-112054200	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr3:112050800-112054200	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr3:112051000-112053600	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr3:112051000-112053800	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr3:112051000-112054000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr3:112051000-112054200	Active TSS	Placenta	Placenta
7	chr3:112051400-112053600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr3:112051400-112053600	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr3:112051400-112053600	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr3:112051400-112054200	Active TSS	Fetal Brain Female	brain
11	chr3:112051400-112054200	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr3:112051400-112054400	Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr3:112051400-112054400	Active TSS	GM12878-XiMat	blood
14	chr3:112051400-112054600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:112051600-112053600	Active TSS	H1 Cell Line	embryonic stem cell
16	chr3:112051600-112053600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:112051600-112053600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:112051600-112053600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:112051600-112053600	Active TSS	Brain Substantia Nigra	brain
20	chr3:112051600-112053600	ZNF genes & repeats	Fetal Brain Male	brain
21	chr3:112051600-112053600	Active TSS	Fetal Thymus	thymus
22	chr3:112051600-112053600	Active TSS	Rectal Mucosa Donor 31	rectum
23	chr3:112051600-112053800	Active TSS	H9 Cell Line	embryonic stem cell
24	chr3:112051600-112053800	Active TSS	Fetal Intestine Small	intestine
25	chr3:112051600-112054000	Active TSS	Aorta	Aorta
26	chr3:112051600-112054000	Active TSS	Fetal Kidney	kidney
27	chr3:112051600-112054000	Active TSS	Fetal Lung	lung
28	chr3:112051600-112054000	Active TSS	Ovary	ovary
29	chr3:112051600-112054200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:112051600-112054200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:112051600-112054200	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr3:112051600-112054200	Active TSS	Thymus	Thymus
33	chr3:112051600-112054400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:112051600-112054400	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr3:112051600-112054400	Active TSS	Brain Angular Gyrus	brain
36	chr3:112051600-112054400	Active TSS	Brain Hippocampus Middle	brain
37	chr3:112051600-112054400	Active TSS	Rectal Smooth Muscle	rectum
38	chr3:112051600-112054800	Active TSS	Brain Cingulate Gyrus	brain
39	chr3:112051800-112053600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr3:112051800-112053600	Active TSS	Colon Smooth Muscle	Colon
41	chr3:112051800-112053800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:112051800-112053800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:112051800-112053800	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr3:112051800-112055400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:112052000-112053600	Active TSS	Primary B cells from peripheral blood	blood
46	chr3:112052000-112053800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:112052200-112053600	Active TSS	Stomach Smooth Muscle	stomach
48	chr3:112052200-112053800	Active TSS	Duodenum Mucosa	Duodenum
49	chr3:112052200-112053800	Active TSS	Fetal Muscle Leg	muscle
50	chr3:112052400-112053600	Active TSS	Colonic Mucosa	Colon

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