Variant report

Variant	rs2865084
Chromosome Location	chr3:178864606-178864607
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr3:178864591-178867744	GM12878	blood:	n/a	n/a
2	CBX3	chr3:178864601-178866202	K562	blood:	n/a	chr3:178865161-178865172
3	HCFC1	chr3:178864527-178868067	Hela-S3	cervix:	n/a	n/a
4	SPI1	chr3:178864550-178865298	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:178788447..178791036-chr3:178864497..178866649,2	MCF-7	breast:
2	chr3:178786925..178790579-chr3:178864297..178867679,5	K562	blood:
3	chr3:178863877..178868371-chr3:178977065..178980370,6	K562	blood:
4	chr3:178864344..178867597-chr3:179039214..179042429,8	K562	blood:
5	chr3:178864465..178866059-chr3:179064181..179066320,2	K562	blood:
6	chr3:178863877..178866682-chr3:178977686..178979355,3	K562	blood:
7	chr3:178864492..178868931-chr3:179039553..179043493,6	MCF-7	breast:
8	chr3:178864291..178867045-chr3:179057738..179060531,2	MCF-7	breast:

No data

Variant related genes	Relation type
PIK3CA	TF binding region
ENSG00000240429	Chromatin interaction
ENSG00000121864	Chromatin interaction
ENSG00000260743	Chromatin interaction
ENSG00000171121	Chromatin interaction
ENSG00000171109	Chromatin interaction
ENSG00000172667	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10936993	0.94[EUR][1000 genomes]
rs12486399	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12497857	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13320527	1.00[CEU][hapmap];0.83[YRI][hapmap];0.94[EUR][1000 genomes]
rs1517585	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28697961	0.94[EUR][1000 genomes]
rs45455192	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4854906	0.94[EUR][1000 genomes]
rs4854940	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4854955	1.00[CEU][hapmap];0.83[YRI][hapmap];0.94[EUR][1000 genomes]
rs4854976	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855094	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60713157	0.84[EUR][1000 genomes]
rs61404287	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61796464	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61796465	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61796466	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61796467	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61798205	0.84[EUR][1000 genomes]
rs61798206	0.84[EUR][1000 genomes]
rs61798207	0.84[EUR][1000 genomes]
rs61798211	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61798213	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6443623	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6791215	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6804195	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs73051979	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73054091	0.90[EUR][1000 genomes]
rs7374077	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7615259	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs950486	0.94[EUR][1000 genomes]
rs9758036	0.84[EUR][1000 genomes]
rs9812252	0.94[EUR][1000 genomes]
rs9819654	0.94[EUR][1000 genomes]
rs9823044	0.83[YRI][hapmap];0.94[EUR][1000 genomes]
rs9833206	0.94[EUR][1000 genomes]
rs9860843	0.96[EUR][1000 genomes]
rs9872959	1.00[CEU][hapmap];0.83[YRI][hapmap];0.94[EUR][1000 genomes]
rs9878005	0.98[EUR][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	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv1792927	chr3:178734558-178877169	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	esv1841799	chr3:178739594-178884337	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv878037	chr3:178825910-178871906	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178861600-178864800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr3:178861600-178864800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:178861800-178864800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:178861800-178864800	Weak transcription	Fetal Kidney	kidney
5	chr3:178864200-178864800	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr3:178864400-178864800	Enhancers	Primary B cells from peripheral blood	blood
7	chr3:178864400-178864800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:178864400-178864800	Weak transcription	Fetal Brain Male	brain
9	chr3:178864400-178864800	Enhancers	Fetal Muscle Trunk	muscle
10	chr3:178864600-178864800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr3:178864600-178864800	Active TSS	Primary monocytes fromperipheralblood	blood
12	chr3:178864600-178864800	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr3:178864600-178864800	Enhancers	Primary hematopoietic stem cells	blood
14	chr3:178864600-178864800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:178864600-178864800	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr3:178864600-178864800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr3:178864600-178864800	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr3:178864600-178864800	Enhancers	Liver	Liver
19	chr3:178864600-178864800	Enhancers	Fetal Heart	heart
20	chr3:178864600-178864800	Enhancers	Fetal Intestine Large	intestine
21	chr3:178864600-178864800	Enhancers	Rectal Smooth Muscle	rectum
22	chr3:178864600-178865000	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr3:178864600-178865000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr3:178864600-178865000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:178864600-178865000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr3:178864600-178865000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr3:178864600-178865000	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr3:178864600-178865000	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr3:178864600-178865000	Flanking Active TSS	Dnd41	blood
30	chr3:178864600-178865000	Flanking Active TSS	Hela-S3	cervix
31	chr3:178864600-178865000	Flanking Active TSS	HUVEC	blood vessel
32	chr3:178864600-178865200	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr3:178864600-178865200	Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr3:178864600-178865200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr3:178864600-178865200	Active TSS	HepG2	liver
36	chr3:178864600-178865200	Flanking Active TSS	NHEK	skin
37	chr3:178864600-178865400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:178864600-178865400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:178864600-178866400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:178864600-178866400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:178864600-178866400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:178864600-178867000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:178864600-178867200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:178864600-178867200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:178864600-178867200	Active TSS	Adipose Nuclei	Adipose
46	chr3:178864600-178867400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:178864600-178867400	Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr3:178864600-178867400	Active TSS	Brain Hippocampus Middle	brain
49	chr3:178864600-178867400	Active TSS	Monocytes-CD14+_RO01746	blood
50	chr3:178864600-178867600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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