Variant report

Variant	rs6825973
Chromosome Location	chr4:144261486-144261487
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	chr4:144254658..144259448-chr4:144261105..144264742,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178972	Chromatin interaction
ENSG00000109458	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17017563	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17017629	1.00[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17017662	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28377860	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28448391	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28676298	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28680635	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72947118	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[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	nsv1033902	chr4:144114413-144285772	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1026110	chr4:144239825-144292148	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144256800-144261600	Active TSS	Aorta	Aorta
2	chr4:144256800-144262000	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr4:144259200-144262600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:144259200-144262600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:144259200-144262600	Weak transcription	Gastric	stomach
6	chr4:144259200-144262600	Weak transcription	Spleen	Spleen
7	chr4:144259200-144264000	Weak transcription	Small Intestine	intestine
8	chr4:144259200-144272400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:144259400-144262600	Weak transcription	Esophagus	oesophagus
10	chr4:144259400-144262600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr4:144259400-144262600	Weak transcription	Lung	lung
12	chr4:144259400-144265400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr4:144259400-144268600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr4:144259400-144272000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:144259400-144272600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr4:144259600-144262600	Weak transcription	Fetal Thymus	thymus
17	chr4:144259600-144264200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr4:144259600-144264200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr4:144259600-144264600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:144259600-144265000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:144259600-144276200	Weak transcription	Fetal Kidney	kidney
22	chr4:144259800-144261800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr4:144259800-144262400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr4:144259800-144262600	Weak transcription	Brain Germinal Matrix	brain
25	chr4:144259800-144264200	Weak transcription	HMEC	breast
26	chr4:144259800-144264600	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr4:144259800-144264800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:144259800-144264800	Weak transcription	Fetal Brain Female	brain
29	chr4:144259800-144265400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:144259800-144268600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr4:144260000-144261600	Enhancers	Fetal Lung	lung
32	chr4:144260000-144262600	Weak transcription	Right Atrium	heart
33	chr4:144260000-144264400	Weak transcription	NHEK	skin
34	chr4:144260000-144267400	Weak transcription	Stomach Mucosa	stomach
35	chr4:144260000-144268600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:144260000-144272800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:144260200-144261600	Enhancers	Adipose Nuclei	Adipose
38	chr4:144260200-144264200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:144260200-144264600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:144260200-144268600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr4:144260400-144263000	Enhancers	Psoas Muscle	Psoas
42	chr4:144260600-144262600	Weak transcription	Left Ventricle	heart
43	chr4:144260800-144261600	Flanking Active TSS	Brain Substantia Nigra	brain
44	chr4:144260800-144261800	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr4:144260800-144262600	Weak transcription	Placenta	Placenta
46	chr4:144260800-144262600	Weak transcription	Pancreas	Pancrea
47	chr4:144261000-144262400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr4:144261000-144262600	Weak transcription	Ovary	ovary
49	chr4:144261000-144264200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:144261000-144264600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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