Variant report

Variant	rs28812220
Chromosome Location	chr3:135984966-135984967
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135912197..135914023-chr3:135984563..135987150,2	MCF-7	breast:
2	chr3:135968510..135970353-chr3:135983958..135985710,2	K562	blood:

Variant related genes	Relation type
ENSG00000114054	Chromatin interaction
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs34523567	0.89[EUR][1000 genomes]
rs35058853	0.93[EUR][1000 genomes]
rs5026242	0.83[EUR][1000 genomes]
rs55797013	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6439638	0.92[EUR][1000 genomes]
rs67214626	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6776841	0.93[EUR][1000 genomes]
rs6783337	0.88[EUR][1000 genomes]
rs6785225	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6796523	0.83[ASN][1000 genomes]
rs7622833	0.93[EUR][1000 genomes]
rs9811261	0.85[EUR][1000 genomes]
rs9811490	0.90[EUR][1000 genomes]
rs9812513	0.93[EUR][1000 genomes]
rs9819496	0.80[EUR][1000 genomes]
rs9826146	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833162	0.93[EUR][1000 genomes]
rs9843348	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9843801	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9853387	0.93[EUR][1000 genomes]
rs9860801	0.90[EUR][1000 genomes]
rs9872326	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv508246	chr3:135922023-136038622	Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv237910	chr3:135983304-135986929	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135970200-135996000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:135970400-135995400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:135970600-135985200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:135970600-135985200	Weak transcription	HMEC	breast
5	chr3:135970600-135987600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:135970600-135998800	Weak transcription	Fetal Brain Male	brain
7	chr3:135970600-135999200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:135970600-135999200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr3:135970600-136039400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:135970800-135986000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:135970800-135995400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:135970800-135998000	Weak transcription	Hela-S3	cervix
13	chr3:135974000-135986800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:135974000-135986800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:135974000-135989400	Strong transcription	Dnd41	blood
16	chr3:135974200-135989600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:135974200-135989600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:135974400-135986400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:135974400-135989600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:135974600-135985200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr3:135974600-135986400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:135974800-135986200	Strong transcription	Placenta	Placenta
23	chr3:135974800-135997800	Weak transcription	Stomach Mucosa	stomach
24	chr3:135975200-135985200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:135975200-135987800	Strong transcription	Fetal Intestine Large	intestine
26	chr3:135975800-135987200	Weak transcription	Thymus	Thymus
27	chr3:135976200-135996000	Weak transcription	Pancreas	Pancrea
28	chr3:135976200-135999400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:135976200-136012400	Weak transcription	NHLF	lung
30	chr3:135976200-136016400	Weak transcription	Colonic Mucosa	Colon
31	chr3:135976200-136021600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:135976400-135989000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr3:135977400-135995600	Weak transcription	Fetal Lung	lung
34	chr3:135977400-135996000	Weak transcription	K562	blood
35	chr3:135977600-135985200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:135977600-135995400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:135977800-135993600	Weak transcription	Fetal Kidney	kidney
38	chr3:135980400-135988000	Strong transcription	Fetal Intestine Small	intestine
39	chr3:135980800-135986000	Weak transcription	A549	lung
40	chr3:135980800-135995000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:135980800-135995600	Weak transcription	Right Ventricle	heart
42	chr3:135980800-135997600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr3:135980800-135999200	Weak transcription	Small Intestine	intestine
44	chr3:135981000-135987600	Weak transcription	Fetal Brain Female	brain
45	chr3:135981000-135995200	Weak transcription	Brain Germinal Matrix	brain
46	chr3:135981000-135995400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr3:135981000-135995400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:135981000-135998600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:135981200-135985000	Weak transcription	Primary B cells from cord blood	blood
50	chr3:135981200-135985000	Weak transcription	Aorta	Aorta

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