Variant report

Variant	rs13092998
Chromosome Location	chr3:119245044-119245045
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119187617..119189310-chr3:119243541..119246268,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176142	Chromatin interaction
ENSG00000163389	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1131265	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12494314	0.95[CHB][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12636784	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2293370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305249	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34844599	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3732421	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57271503	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62264485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650774	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9843355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9855065	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9884090	0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119220200-119246800	Weak transcription	Stomach Mucosa	stomach
2	chr3:119221400-119245400	Strong transcription	Placenta	Placenta
3	chr3:119222000-119245400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr3:119224000-119245200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr3:119226000-119245200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:119226000-119245200	Strong transcription	Liver	Liver
7	chr3:119226600-119245200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:119227400-119245400	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:119228000-119250000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:119230600-119245400	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr3:119231800-119245400	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:119231800-119257200	Strong transcription	GM12878-XiMat	blood
13	chr3:119232000-119245200	Strong transcription	A549	lung
14	chr3:119233000-119245200	Strong transcription	Duodenum Mucosa	Duodenum
15	chr3:119237600-119245200	Strong transcription	Fetal Thymus	thymus
16	chr3:119237800-119245400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:119237800-119245800	Weak transcription	Small Intestine	intestine
18	chr3:119237800-119246000	Weak transcription	Right Ventricle	heart
19	chr3:119237800-119246400	Weak transcription	Pancreas	Pancrea
20	chr3:119237800-119246600	Weak transcription	Esophagus	oesophagus
21	chr3:119237800-119248000	Weak transcription	Aorta	Aorta
22	chr3:119237800-119251400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:119237800-119255800	Weak transcription	Spleen	Spleen
24	chr3:119238000-119245200	Strong transcription	Dnd41	blood
25	chr3:119238000-119245400	Strong transcription	Fetal Muscle Leg	muscle
26	chr3:119238000-119248400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:119238200-119245200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:119238200-119245200	Strong transcription	Fetal Lung	lung
29	chr3:119238200-119245800	Weak transcription	NHEK	skin
30	chr3:119238200-119249000	Weak transcription	NHLF	lung
31	chr3:119238800-119246800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:119239600-119248400	Weak transcription	HSMMtube	muscle
33	chr3:119239600-119253000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:119239800-119245400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr3:119239800-119247400	Weak transcription	Fetal Heart	heart
36	chr3:119239800-119252400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:119240200-119245200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:119240200-119248600	Weak transcription	Fetal Brain Male	brain
39	chr3:119240400-119246000	Weak transcription	Ovary	ovary
40	chr3:119240600-119245800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:119240600-119245800	Weak transcription	Fetal Intestine Small	intestine
42	chr3:119240600-119245800	Weak transcription	Psoas Muscle	Psoas
43	chr3:119240600-119246600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr3:119240600-119246600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:119240600-119247400	Strong transcription	Primary B cells from peripheral blood	blood
46	chr3:119240600-119249400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:119242000-119245400	Strong transcription	Thymus	Thymus
48	chr3:119242200-119245200	Strong transcription	Left Ventricle	heart
49	chr3:119242400-119246400	Weak transcription	Gastric	stomach
50	chr3:119242400-119246800	Weak transcription	Colon Smooth Muscle	Colon

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