Variant report

Variant	rs73878329
Chromosome Location	chr3:161133589-161133590
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160786404..160789728-chr3:161132273..161134989,3	MCF-7	breast:
2	chr3:161003253..161016100-chr3:161121496..161137189,33	MCF-7	breast:
3	chr3:160821926..160824694-chr3:161130720..161134424,3	MCF-7	breast:
4	chr12:53441527..53442038-chr3:161133367..161134304,2	Hela-S3	cervix:
5	chr3:160934874..160951087-chr3:161118055..161142485,77	MCF-7	breast:
6	chr3:160937705..160941241-chr3:161127569..161134417,11	MCF-7	breast:
7	chr3:161031194..161033997-chr3:161131950..161133763,3	MCF-7	breast:
8	chr17:59472839..59476239-chr3:161133074..161135554,3	MCF-7	breast:
9	chr3:161040559..161042979-chr3:161133154..161135842,2	MCF-7	breast:
10	chr3:161007555..161015806-chr3:161127103..161142651,19	MCF-7	breast:
11	chr17:7387105..7389788-chr3:161131075..161133890,2	MCF-7	breast:
12	chr17:57922421..57925023-chr3:161131706..161133693,2	MCF-7	breast:
13	chr3:102426713..102428233-chr3:161131598..161134258,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000169255	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000169251	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12486111	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12486998	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12487002	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12488127	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12491623	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12494520	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13319558	0.85[AMR][1000 genomes]
rs1450518	0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2035499	0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2306209	0.85[AMR][1000 genomes]
rs56839556	0.94[ASN][1000 genomes]
rs58851337	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs58892449	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59193340	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs59368066	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6441375	0.82[AMR][1000 genomes]
rs6781086	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6787697	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6793980	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73878309	0.85[AMR][1000 genomes]
rs73878320	0.81[AFR][1000 genomes]
rs73878323	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7614130	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7629841	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7651924	0.82[AMR][1000 genomes]
rs9822705	0.85[AMR][1000 genomes]
rs9851699	0.82[AMR][1000 genomes]
rs9855572	0.82[AMR][1000 genomes]
rs9860980	0.85[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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv877710	chr3:161087857-161245414	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161125600-161137000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:161128200-161133600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:161128200-161134000	Weak transcription	Esophagus	oesophagus
4	chr3:161129600-161134600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:161130600-161134800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr3:161131400-161133800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:161131600-161133600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:161131600-161133600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:161131600-161134000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:161131600-161134000	Weak transcription	Right Atrium	heart
11	chr3:161131600-161134200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:161131600-161140000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:161131800-161133800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:161131800-161133800	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:161131800-161134000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:161131800-161134000	Weak transcription	Aorta	Aorta
17	chr3:161131800-161134000	Weak transcription	Brain Angular Gyrus	brain
18	chr3:161131800-161134000	Weak transcription	Pancreas	Pancrea
19	chr3:161131800-161134000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:161131800-161134200	Weak transcription	Left Ventricle	heart
21	chr3:161131800-161134200	Weak transcription	NHLF	lung
22	chr3:161132000-161133600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:161132400-161134000	Enhancers	NH-A	brain
24	chr3:161132400-161134400	Enhancers	Adipose Nuclei	Adipose
25	chr3:161132400-161134600	Enhancers	Stomach Mucosa	stomach
26	chr3:161132800-161133600	Enhancers	Osteobl	bone
27	chr3:161132800-161134000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:161132800-161134000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:161132800-161134000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:161132800-161134200	Enhancers	Hela-S3	cervix
31	chr3:161132800-161134600	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr3:161132800-161134600	Enhancers	NHDF-Ad	bronchial
33	chr3:161133000-161134600	Enhancers	Muscle Satellite Cultured Cells	--
34	chr3:161133200-161133800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:161133200-161133800	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr3:161133200-161134200	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr3:161133200-161134400	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr3:161133200-161134600	Enhancers	Liver	Liver
39	chr3:161133200-161134600	Enhancers	HMEC	breast
40	chr3:161133200-161134600	Enhancers	NHEK	skin
41	chr3:161133400-161133600	Enhancers	H1 Cell Line	embryonic stem cell
42	chr3:161133400-161133600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:161133400-161133800	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr3:161133400-161133800	Enhancers	Brain Anterior Caudate	brain
45	chr3:161133400-161133800	Enhancers	Brain Substantia Nigra	brain
46	chr3:161133400-161134400	Enhancers	Brain Hippocampus Middle	brain
47	chr3:161133400-161134400	Enhancers	Fetal Lung	lung
48	chr3:161133400-161134400	Enhancers	Stomach Smooth Muscle	stomach
49	chr3:161133400-161134400	Flanking Active TSS	HUVEC	blood vessel
50	chr3:161133400-161134600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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