Variant report

Variant	rs60238096
Chromosome Location	chr3:113676681-113676682
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	chr3:113666438..113668276-chr3:113676676..113680179,3	MCF-7	breast:
2	chr3:113665870..113669874-chr3:113673727..113678562,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273394	Chromatin interaction
ENSG00000184307	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10804511	1.00[AMR][1000 genomes]
rs2566981	1.00[AMR][1000 genomes]
rs2566984	1.00[AMR][1000 genomes]
rs2566985	1.00[AMR][1000 genomes]
rs4359785	1.00[AMR][1000 genomes]
rs59292926	1.00[AMR][1000 genomes]
rs6781200	1.00[AMR][1000 genomes]
rs6799923	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6800121	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952678	1.00[AMR][1000 genomes]
rs72952679	1.00[AMR][1000 genomes]
rs72952680	1.00[AMR][1000 genomes]
rs72952687	1.00[AMR][1000 genomes]
rs72954664	1.00[AMR][1000 genomes]
rs72954670	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72954674	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72954676	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72954680	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72954688	1.00[AMR][1000 genomes]
rs7628645	1.00[AMR][1000 genomes]
rs7646432	1.00[AMR][1000 genomes]
rs7650388	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7650416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113667600-113695800	Weak transcription	Left Ventricle	heart
2	chr3:113667800-113679600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:113667800-113683000	Weak transcription	Small Intestine	intestine
4	chr3:113667800-113683400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:113667800-113685000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:113667800-113685200	Weak transcription	A549	lung
7	chr3:113667800-113696800	Weak transcription	Right Ventricle	heart
8	chr3:113667800-113710800	Weak transcription	Esophagus	oesophagus
9	chr3:113668000-113680000	Weak transcription	Hela-S3	cervix
10	chr3:113668000-113687800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:113668000-113692000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:113668000-113699000	Weak transcription	Stomach Mucosa	stomach
13	chr3:113668200-113696200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:113668400-113724200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:113669600-113679600	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr3:113670200-113681400	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:113670600-113681200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:113671600-113680000	Strong transcription	Duodenum Mucosa	Duodenum
19	chr3:113672000-113685600	Strong transcription	Primary B cells from cord blood	blood
20	chr3:113672200-113679800	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:113672400-113698000	Weak transcription	Ovary	ovary
22	chr3:113673000-113679000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr3:113673000-113700800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:113673200-113676800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:113673200-113682000	Weak transcription	Dnd41	blood
26	chr3:113673200-113683400	Weak transcription	Fetal Thymus	thymus
27	chr3:113673200-113683400	Weak transcription	Lung	lung
28	chr3:113673200-113685200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:113673200-113688600	Weak transcription	Spleen	Spleen
30	chr3:113673400-113677200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:113673400-113679000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:113673400-113683000	Weak transcription	Primary T cells from cord blood	blood
33	chr3:113673400-113687600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:113673400-113696400	Weak transcription	Brain Angular Gyrus	brain
35	chr3:113673400-113704400	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:113673400-113761000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr3:113674000-113743800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:113674200-113676800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:113674200-113678000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:113674200-113685800	Weak transcription	Brain Anterior Caudate	brain
41	chr3:113674400-113677200	Weak transcription	Aorta	Aorta
42	chr3:113674800-113682200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr3:113675200-113679600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:113675200-113680200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:113675200-113680800	Strong transcription	Liver	Liver
46	chr3:113675400-113676800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:113675400-113677000	Strong transcription	Primary hematopoietic stem cells	blood
48	chr3:113675400-113677400	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr3:113675600-113679200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:113675600-113679400	Strong transcription	HUES64 Cell Line	embryonic stem cell

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