Variant report

Variant	rs12498609
Chromosome Location	chr4:106155185-106155186
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106060509..106062315-chr4:106155058..106156816,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251259	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1114718	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11933960	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12506006	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12511800	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12640842	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12642165	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12647779	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12647884	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1391442	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17583579	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17583593	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17616993	0.84[EUR][1000 genomes]
rs2023841	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2088484	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2866774	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34485921	0.83[AFR][1000 genomes]
rs6533180	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs949681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9637601	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106113600-106173800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr4:106113600-106195800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr4:106114400-106155200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr4:106114600-106155600	Weak transcription	Esophagus	oesophagus
5	chr4:106118000-106155400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr4:106118800-106155200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:106127600-106155400	Weak transcription	Placenta	Placenta
8	chr4:106127800-106155200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:106127800-106155200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:106136000-106157400	Weak transcription	Right Ventricle	heart
11	chr4:106136800-106155200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr4:106137000-106155200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:106137400-106155200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr4:106137600-106155400	Weak transcription	HSMM	muscle
15	chr4:106137600-106155600	Weak transcription	Fetal Intestine Small	intestine
16	chr4:106138400-106155200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:106139000-106155200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr4:106139200-106155200	Weak transcription	Fetal Intestine Large	intestine
19	chr4:106141000-106155600	Weak transcription	Gastric	stomach
20	chr4:106142000-106155400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr4:106142000-106190800	Weak transcription	Small Intestine	intestine
22	chr4:106145600-106155200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:106145600-106155200	Weak transcription	Fetal Kidney	kidney
24	chr4:106145600-106155200	Weak transcription	Ovary	ovary
25	chr4:106145600-106155400	Weak transcription	Fetal Brain Female	brain
26	chr4:106145600-106155600	Weak transcription	Brain Substantia Nigra	brain
27	chr4:106145600-106167400	Weak transcription	NHDF-Ad	bronchial
28	chr4:106145800-106155200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:106145800-106155600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr4:106145800-106155800	Weak transcription	Brain Anterior Caudate	brain
31	chr4:106146000-106155200	Weak transcription	Adipose Nuclei	Adipose
32	chr4:106146600-106155400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:106146800-106155200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr4:106146800-106155200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr4:106146800-106157400	Weak transcription	Fetal Heart	heart
36	chr4:106147000-106155200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr4:106147000-106155200	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:106147000-106155200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr4:106147000-106156200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr4:106147400-106155400	Weak transcription	Brain Hippocampus Middle	brain
41	chr4:106147400-106155600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr4:106147800-106155200	Weak transcription	Brain Germinal Matrix	brain
43	chr4:106147800-106155200	Weak transcription	Spleen	Spleen
44	chr4:106147800-106155600	Weak transcription	Lung	lung
45	chr4:106147800-106156800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:106148000-106155200	Weak transcription	Pancreas	Pancrea
47	chr4:106148000-106155600	Weak transcription	Brain Angular Gyrus	brain
48	chr4:106148000-106192800	Weak transcription	Psoas Muscle	Psoas
49	chr4:106148600-106155600	Weak transcription	Fetal Brain Male	brain
50	chr4:106150200-106191400	Weak transcription	HUVEC	blood vessel

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