Variant report

Variant	rs16860075
Chromosome Location	chr3:112530890-112530891
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112529420..112531231-chr3:112543770..112545710,2	MCF-7	breast:
2	chr3:112451598..112455262-chr3:112529642..112532611,4	MCF-7	breast:
3	chr3:112355777..112361345-chr3:112530635..112535712,9	MCF-7	breast:
4	chr3:112519716..112521811-chr3:112528431..112531172,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242770	Chromatin interaction
ENSG00000091986	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1125377	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11918522	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11918738	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860073	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[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]
rs16860127	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs16860128	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs16860141	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1873041	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs1948164	0.91[ASN][1000 genomes]
rs2078008	1.00[CHB][hapmap]
rs4682117	0.94[ASN][1000 genomes]
rs4682119	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4682432	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66635385	0.94[ASN][1000 genomes]
rs6809029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6809039	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7625445	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7625533	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7637319	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv432477	chr3:112390310-112603310	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv877343	chr3:112470586-112597706	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112521600-112531600	Weak transcription	Stomach Mucosa	stomach
2	chr3:112527000-112531000	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr3:112527000-112531200	Weak transcription	Primary T cells from cord blood	blood
4	chr3:112527400-112532600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr3:112527600-112531000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:112528800-112533600	Enhancers	Placenta Amnion	Placenta Amnion
7	chr3:112529200-112531000	Enhancers	Fetal Kidney	kidney
8	chr3:112529200-112533200	Enhancers	Colon Smooth Muscle	Colon
9	chr3:112529200-112533600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:112529400-112531200	Enhancers	HSMM	muscle
11	chr3:112529400-112533200	Enhancers	Rectal Smooth Muscle	rectum
12	chr3:112529400-112533200	Enhancers	NHLF	lung
13	chr3:112529400-112533400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:112529600-112531000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:112529600-112531400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:112529600-112531400	Enhancers	Osteobl	bone
17	chr3:112529600-112531600	Enhancers	Fetal Stomach	stomach
18	chr3:112529600-112533600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:112529800-112531400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:112529800-112533200	Enhancers	HSMMtube	muscle
21	chr3:112529800-112534000	Enhancers	A549	lung
22	chr3:112530000-112531000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:112530000-112531000	Enhancers	Esophagus	oesophagus
24	chr3:112530000-112531000	Enhancers	Ovary	ovary
25	chr3:112530000-112531200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:112530000-112531200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:112530000-112531200	Enhancers	Fetal Muscle Trunk	muscle
28	chr3:112530000-112531200	Enhancers	Fetal Muscle Leg	muscle
29	chr3:112530000-112531200	Enhancers	NH-A	brain
30	chr3:112530000-112533000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:112530000-112533000	Enhancers	K562	blood
32	chr3:112530200-112533600	Enhancers	NHDF-Ad	bronchial
33	chr3:112530200-112533800	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr3:112530200-112538800	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr3:112530400-112531000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:112530400-112531000	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr3:112530400-112532200	Weak transcription	Aorta	Aorta
38	chr3:112530400-112532800	Enhancers	Primary B cells from cord blood	blood
39	chr3:112530400-112534000	Enhancers	Primary B cells from peripheral blood	blood
40	chr3:112530600-112531000	Enhancers	Muscle Satellite Cultured Cells	--
41	chr3:112530600-112531200	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr3:112530600-112531400	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr3:112530600-112532000	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr3:112530600-112533600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:112530800-112531000	Enhancers	Primary hematopoietic stem cells	blood
46	chr3:112530800-112531000	Flanking Active TSS	Fetal Lung	lung
47	chr3:112530800-112531000	Enhancers	Right Atrium	heart
48	chr3:112530800-112531000	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr3:112530800-112531000	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr3:112530800-112531200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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