Variant report

Variant	rs6440054
Chromosome Location	chr3:141678347-141678348
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141670066..141671799-chr3:141678261..141680634,2	K562	blood:
2	chr3:141677833..141681562-chr3:141940818..141944357,3	MCF-7	breast:
3	chr3:141676954..141678709-chr3:141680437..141684558,4	K562	blood:

Variant related genes	Relation type
ENSG00000175066	Chromatin interaction
ENSG00000114126	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1045279	0.87[EUR][1000 genomes]
rs10804681	0.82[EUR][1000 genomes]
rs11569216	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11569256	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13081914	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2861421	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34092379	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34486172	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34773643	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3811708	0.81[EUR][1000 genomes]
rs4315664	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4315665	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62283132	0.81[EUR][1000 genomes]
rs6440053	0.82[EUR][1000 genomes]
rs9815587	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9942	0.87[EUR][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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141629000-141739200	Weak transcription	Psoas Muscle	Psoas
2	chr3:141634200-141682000	Weak transcription	Brain Angular Gyrus	brain
3	chr3:141644800-141678400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr3:141659200-141696200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:141659400-141678400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:141659600-141678400	Weak transcription	A549	lung
7	chr3:141660600-141698200	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr3:141666000-141697600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:141666400-141687200	Strong transcription	Dnd41	blood
10	chr3:141667000-141685600	Weak transcription	Brain Substantia Nigra	brain
11	chr3:141668000-141686600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:141668600-141678400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:141668600-141688600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:141669600-141696800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr3:141670000-141683600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:141670000-141684000	Weak transcription	Colonic Mucosa	Colon
17	chr3:141670200-141681200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:141671600-141697400	Weak transcription	Gastric	stomach
19	chr3:141671800-141681600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:141671800-141681800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr3:141671800-141682200	Weak transcription	Pancreas	Pancrea
22	chr3:141671800-141682400	Weak transcription	Lung	lung
23	chr3:141671800-141686400	Weak transcription	HepG2	liver
24	chr3:141671800-141691200	Weak transcription	Spleen	Spleen
25	chr3:141671800-141719000	Weak transcription	Placenta	Placenta
26	chr3:141671800-141724000	Weak transcription	Right Ventricle	heart
27	chr3:141671800-141735600	Weak transcription	Aorta	Aorta
28	chr3:141672000-141697000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr3:141672000-141700000	Weak transcription	Small Intestine	intestine
30	chr3:141672400-141681600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:141672400-141688600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:141674400-141678400	Weak transcription	Ovary	ovary
33	chr3:141674400-141678600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:141674400-141679200	Weak transcription	Brain Germinal Matrix	brain
35	chr3:141674400-141680800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:141674400-141682000	Weak transcription	Brain Hippocampus Middle	brain
37	chr3:141674400-141682200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:141674400-141688000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:141674400-141690200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:141674400-141708000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr3:141674600-141678400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:141674600-141678400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:141674600-141678600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:141674600-141678600	Weak transcription	Colon Smooth Muscle	Colon
45	chr3:141674600-141700400	Weak transcription	Esophagus	oesophagus
46	chr3:141674600-141712600	Weak transcription	Fetal Brain Male	brain
47	chr3:141674800-141678400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:141674800-141679200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:141674800-141679200	Weak transcription	Fetal Brain Female	brain
50	chr3:141675000-141678400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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