Variant report

Variant	rs16860025
Chromosome Location	chr3:112494025-112494026
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	chr3:112488625..112490869-chr3:112493684..112496164,2	MCF-7	breast:
2	chr3:112492371..112494990-chr3:112495868..112498193,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12633641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12634296	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636634	1.00[AFR][1000 genomes]
rs1488590	0.91[AFR][1000 genomes]
rs16859996	0.91[AFR][1000 genomes]
rs16860034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036938	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2087286	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895405	0.91[AFR][1000 genomes]
rs4682421	0.82[CHB][hapmap]
rs4682422	1.00[CEU][hapmap]
rs4682423	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[AFR][1000 genomes]
rs4682425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682427	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682428	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611048	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7648520	1.00[ASN][1000 genomes]
rs7650843	0.88[AMR][1000 genomes]

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:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112485800-112494400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:112488000-112501200	Enhancers	NHLF	lung
3	chr3:112490000-112495200	Enhancers	Primary T cells fromperipheralblood	blood
4	chr3:112490000-112495200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:112490200-112494800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:112490200-112495600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:112490200-112499800	Weak transcription	K562	blood
8	chr3:112491000-112494800	Enhancers	Stomach Mucosa	stomach
9	chr3:112491200-112494600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:112491200-112495200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:112491200-112495200	Enhancers	Hela-S3	cervix
12	chr3:112491200-112495600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:112491200-112499600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:112491200-112501200	Enhancers	NHDF-Ad	bronchial
15	chr3:112491400-112494800	Enhancers	Fetal Muscle Leg	muscle
16	chr3:112491600-112495200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:112492000-112494200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:112492000-112498000	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:112492200-112495000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:112492200-112495200	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr3:112492200-112495200	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr3:112492200-112495600	Enhancers	Primary B cells from peripheral blood	blood
23	chr3:112492200-112501600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:112492200-112502000	Enhancers	NHEK	skin
25	chr3:112492400-112495200	Enhancers	Primary B cells from cord blood	blood
26	chr3:112492400-112495200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr3:112492400-112495600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:112492800-112495000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:112492800-112495000	Flanking Active TSS	A549	lung
30	chr3:112492800-112495200	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr3:112492800-112495200	Enhancers	Adipose Nuclei	Adipose
32	chr3:112492800-112495400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:112492800-112501000	Enhancers	HMEC	breast
34	chr3:112492800-112501000	Enhancers	HSMM	muscle
35	chr3:112492800-112501200	Enhancers	Osteobl	bone
36	chr3:112493000-112494800	Enhancers	HSMMtube	muscle
37	chr3:112493000-112495200	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr3:112493000-112495200	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr3:112493000-112495200	Enhancers	NH-A	brain
40	chr3:112493000-112496600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:112493000-112500000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:112493000-112500800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:112493200-112494400	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr3:112493200-112498800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:112493400-112495000	Weak transcription	Fetal Thymus	thymus
46	chr3:112493600-112494200	Enhancers	Rectal Smooth Muscle	rectum
47	chr3:112493600-112494200	Enhancers	Right Atrium	heart
48	chr3:112493600-112494400	Enhancers	Fetal Stomach	stomach
49	chr3:112493600-112494800	Weak transcription	Primary T cells from cord blood	blood
50	chr3:112493600-112495200	Enhancers	Esophagus	oesophagus

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