Variant report

Variant	rs9854720
Chromosome Location	chr3:134027322-134027323
allele	A/G
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:28)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:28 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:134026945..134027852-chr3:134172592..134173161,2	MCF-7	breast:
2	chr3:134024378..134037377-chr3:134063304..134080412,83	MCF-7	breast:
3	chr3:134026923..134027850-chr3:134198250..134199054,2	MCF-7	breast:
4	chr3:134027115..134027630-chr3:134100230..134100993,2	MCF-7	breast:
5	chr3:134026993..134027640-chr3:134210825..134211549,2	K562	blood:
6	chr3:134027019..134027846-chr3:134191593..134192140,2	K562	blood:
7	chr3:134026032..134027592-chr3:134187039..134189717,2	MCF-7	breast:
8	chr3:134024307..134037207-chr3:134080573..134100993,88	MCF-7	breast:
9	chr3:134026198..134027834-chr3:134167829..134169129,15	MCF-7	breast:
10	chr3:134026977..134027845-chr3:134096964..134097732,3	MCF-7	breast:
11	chr3:134026974..134027562-chr3:134085957..134086628,2	MCF-7	breast:
12	chr3:134027016..134027584-chr3:134082632..134083298,2	MCF-7	breast:
13	chr3:134026656..134027867-chr3:134192501..134193467,17	MCF-7	breast:
14	chr3:134027313..134027882-chr3:134096935..134097746,2	K562	blood:
15	chr3:134026309..134027866-chr3:134192546..134193488,7	MCF-7	breast:
16	chr3:134020415..134022058-chr3:134026557..134028767,2	MCF-7	breast:
17	chr3:134026798..134028420-chr3:134164621..134166613,2	MCF-7	breast:
18	chr3:134026969..134027956-chr3:134096702..134097867,13	MCF-7	breast:
19	chr3:134027318..134027903-chr3:134092861..134093553,2	MCF-7	breast:
20	chr3:134026968..134027634-chr3:134090071..134090721,3	MCF-7	breast:
21	chr3:134026973..134027620-chr3:134211228..134212162,3	MCF-7	breast:
22	chr3:134026947..134027640-chr3:134198061..134198841,2	MCF-7	breast:
23	chr3:134027292..134027808-chr3:134092974..134093743,2	MCF-7	breast:
24	chr3:134025588..134027447-chr3:134198814..134200765,2	MCF-7	breast:
25	chr3:134027278..134027877-chr3:134192552..134193439,4	K562	blood:
26	chr3:134026918..134027856-chr3:134172237..134173017,2	K562	blood:
27	chr3:134026273..134028991-chr3:134194363..134198560,4	MCF-7	breast:
28	chr3:134027069..134028938-chr3:134191393..134194235,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000214289	Chromatin interaction
ENSG00000260633	Chromatin interaction
ENSG00000114019	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10935111	0.96[ASN][1000 genomes]
rs10935112	1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4308248	0.87[EUR][1000 genomes]
rs4499567	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4682660	0.83[ASN][1000 genomes]
rs4682662	0.83[GIH][hapmap];0.93[MKK][hapmap];0.87[YRI][hapmap]
rs62271223	0.94[ASN][1000 genomes]
rs6786265	0.83[CEU][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs6810377	0.84[CEU][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs9843732	0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs9849839	0.82[EUR][1000 genomes]
rs9861832	0.92[EUR][1000 genomes]
rs9881414	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9854720	TF	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134023800-134032400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:134025200-134031600	Weak transcription	Ovary	ovary
3	chr3:134025600-134030800	Weak transcription	Spleen	Spleen
4	chr3:134026000-134028600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:134026000-134029200	Enhancers	HMEC	breast
6	chr3:134026200-134028400	Enhancers	NHEK	skin
7	chr3:134026400-134028800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:134026400-134029400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:134026400-134031800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:134026600-134027800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr3:134026800-134027400	Flanking Active TSS	Brain Hippocampus Middle	brain
12	chr3:134026800-134027400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr3:134026800-134027600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr3:134026800-134027600	Enhancers	Esophagus	oesophagus
15	chr3:134026800-134027600	Enhancers	Gastric	stomach
16	chr3:134026800-134027800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:134026800-134027800	Flanking Active TSS	HepG2	liver
18	chr3:134026800-134028000	Enhancers	Placenta Amnion	Placenta Amnion
19	chr3:134026800-134029400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr3:134026800-134030400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:134026800-134031800	Enhancers	HSMM	muscle
22	chr3:134026800-134032400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:134026800-134034800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:134027000-134027400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:134027000-134027400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:134027000-134027400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:134027000-134027400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:134027000-134027400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr3:134027000-134027400	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr3:134027000-134027400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:134027000-134027400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr3:134027000-134027400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr3:134027000-134027400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:134027000-134027400	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr3:134027000-134027400	Flanking Active TSS	Brain Angular Gyrus	brain
36	chr3:134027000-134027400	Flanking Active TSS	Brain Cingulate Gyrus	brain
37	chr3:134027000-134027400	Active TSS	Brain Germinal Matrix	brain
38	chr3:134027000-134027400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
39	chr3:134027000-134027400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:134027000-134027400	Flanking Active TSS	Brain Substantia Nigra	brain
41	chr3:134027000-134027400	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr3:134027000-134027400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr3:134027000-134027400	Enhancers	Fetal Brain Female	brain
44	chr3:134027000-134027400	Flanking Active TSS	Fetal Kidney	kidney
45	chr3:134027000-134027400	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr3:134027000-134027400	Flanking Active TSS	Fetal Lung	lung
47	chr3:134027000-134027400	Active TSS	Fetal Muscle Trunk	muscle
48	chr3:134027000-134027400	Flanking Active TSS	Rectal Smooth Muscle	rectum
49	chr3:134027000-134027400	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr3:134027000-134027400	Flanking Active TSS	A549	lung

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