Variant report

Variant	rs62248848
Chromosome Location	chr3:42660862-42660863
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42659807..42662376-chr3:42694804..42697042,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230084	Chromatin interaction
ENSG00000114853	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1266699	1.00[ASN][1000 genomes]
rs62246639	1.00[ASN][1000 genomes]
rs62248806	1.00[ASN][1000 genomes]
rs62248843	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62248845	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635021	0.88[AMR][1000 genomes];0.84[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	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv876730	chr3:42643935-42667936	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42643200-42672800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:42643600-42675000	Weak transcription	Aorta	Aorta
3	chr3:42643800-42671200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:42644000-42671000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:42644000-42671200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:42644000-42671400	Weak transcription	HSMMtube	muscle
7	chr3:42644000-42672000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:42644200-42663200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:42644200-42672400	Weak transcription	Fetal Kidney	kidney
10	chr3:42646000-42672000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:42647000-42671400	Weak transcription	NHEK	skin
12	chr3:42647200-42668600	Weak transcription	Brain Germinal Matrix	brain
13	chr3:42647200-42688200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr3:42647400-42672000	Weak transcription	NHLF	lung
15	chr3:42647600-42672000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:42647600-42677600	Weak transcription	Gastric	stomach
17	chr3:42648800-42672600	Weak transcription	Fetal Brain Female	brain
18	chr3:42649800-42671200	Weak transcription	Fetal Brain Male	brain
19	chr3:42650400-42671400	Weak transcription	Thymus	Thymus
20	chr3:42650400-42671800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:42650400-42672000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:42650600-42669400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:42650600-42669400	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:42650600-42672600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:42650600-42673000	Weak transcription	Esophagus	oesophagus
26	chr3:42650800-42663200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:42650800-42672800	Weak transcription	Ovary	ovary
28	chr3:42651200-42693000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:42651400-42671000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:42651800-42680400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:42653400-42672000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:42653600-42661800	Weak transcription	Spleen	Spleen
33	chr3:42653600-42672600	Weak transcription	Lung	lung
34	chr3:42653600-42672600	Weak transcription	Pancreas	Pancrea
35	chr3:42654200-42661800	Weak transcription	Brain Anterior Caudate	brain
36	chr3:42655000-42672400	Weak transcription	Right Ventricle	heart
37	chr3:42655000-42677800	Weak transcription	Small Intestine	intestine
38	chr3:42655200-42672000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:42655400-42661000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr3:42655400-42665200	Weak transcription	GM12878-XiMat	blood
41	chr3:42655400-42672000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:42655400-42674400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr3:42656200-42663400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:42656200-42688400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr3:42656600-42673000	Strong transcription	Hela-S3	cervix
46	chr3:42657200-42663200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr3:42657200-42663200	Weak transcription	Colon Smooth Muscle	Colon
48	chr3:42657400-42663800	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr3:42657400-42667200	Strong transcription	Osteobl	bone
50	chr3:42657400-42679600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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