Variant report

Variant	rs9861344
Chromosome Location	chr3:119307553-119307554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119298069..119302115-chr3:119304955..119308560,6	MCF-7	breast:
2	chr3:119305600..119307838-chr3:119310497..119312054,2	K562	blood:
3	chr3:119297063..119300617-chr3:119303800..119308221,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144843	Chromatin interaction
ENSG00000272967	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11915800	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11918611	1.00[EUR][1000 genomes]
rs11919422	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11927159	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11927863	1.00[EUR][1000 genomes]
rs12106815	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12106869	1.00[EUR][1000 genomes]
rs13317715	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16830032	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs58318736	1.00[EUR][1000 genomes]
rs61575899	1.00[EUR][1000 genomes]
rs6767853	1.00[EUR][1000 genomes]
rs72968486	1.00[EUR][1000 genomes]
rs73854857	1.00[EUR][1000 genomes]
rs73857025	1.00[EUR][1000 genomes]
rs7611869	1.00[EUR][1000 genomes]
rs9821005	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9860332	1.00[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9861284	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9866191	1.00[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9876397	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9876408	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9876504	0.86[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9881550	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv3963	chr3:119301064-119345904	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv522542	chr3:119306930-119309260	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	2 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	chr3:119299200-119307800	Weak transcription	Esophagus	oesophagus
2	chr3:119299200-119308000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:119299200-119314600	Weak transcription	Ovary	ovary
4	chr3:119299200-119315000	Weak transcription	Gastric	stomach
5	chr3:119299400-119307800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:119299400-119314200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:119299400-119314400	Weak transcription	Brain Angular Gyrus	brain
8	chr3:119299600-119307800	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:119299600-119308000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:119299600-119314200	Weak transcription	Brain Substantia Nigra	brain
11	chr3:119299600-119314200	Weak transcription	Psoas Muscle	Psoas
12	chr3:119299800-119308000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:119299800-119308000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:119299800-119309200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:119299800-119314600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:119299800-119314600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:119299800-119318000	Weak transcription	Fetal Heart	heart
18	chr3:119301400-119307800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:119303400-119308200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:119303400-119308200	Strong transcription	Aorta	Aorta
21	chr3:119303600-119308600	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr3:119303600-119309800	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr3:119304000-119308800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:119304800-119309000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:119305000-119308200	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr3:119305200-119308000	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:119305400-119307600	Strong transcription	Fetal Muscle Leg	muscle
28	chr3:119305400-119307600	Enhancers	HSMM	muscle
29	chr3:119305400-119308200	Strong transcription	Stomach Smooth Muscle	stomach
30	chr3:119305400-119314400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:119305600-119307600	Weak transcription	Left Ventricle	heart
32	chr3:119305600-119309400	Weak transcription	Fetal Stomach	stomach
33	chr3:119305600-119314200	Weak transcription	Lung	lung
34	chr3:119305600-119314200	Weak transcription	HSMMtube	muscle
35	chr3:119305800-119307600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:119305800-119314600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:119306000-119316800	Weak transcription	Pancreas	Pancrea
38	chr3:119306200-119307800	Enhancers	Primary B cells from cord blood	blood
39	chr3:119306200-119308800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr3:119306400-119308400	Enhancers	Primary B cells from peripheral blood	blood
41	chr3:119306600-119307800	Genic enhancers	Adipose Nuclei	Adipose
42	chr3:119306600-119314200	Weak transcription	Right Ventricle	heart
43	chr3:119306800-119307600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
44	chr3:119306800-119308600	Enhancers	Osteobl	bone
45	chr3:119307200-119307600	Enhancers	Duodenum Mucosa	Duodenum
46	chr3:119307200-119307600	Enhancers	Fetal Intestine Small	intestine
47	chr3:119307200-119307600	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr3:119307200-119307800	Enhancers	Primary hematopoietic stem cells	blood
49	chr3:119307200-119307800	Strong transcription	Fetal Lung	lung
50	chr3:119307200-119308200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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