Variant report

Variant	rs342518
Chromosome Location	chr3:42531939-42531940
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42529189..42533440-chr3:42542111..42547805,7	MCF-7	breast:
2	chr3:42531149..42533028-chr3:42536524..42539427,2	K562	blood:
3	chr3:42530826..42532849-chr3:42845908..42847611,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181061	Chromatin interaction
ENSG00000144648	Chromatin interaction
ENSG00000114812	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs342519	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs342531	0.88[AMR][1000 genomes]
rs418252	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs418736	0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs419555	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs421031	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs427048	0.96[AMR][1000 genomes]
rs427845	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs435698	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs452906	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs478581	0.96[AMR][1000 genomes]
rs493215	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs568717	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs569417	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs589328	0.95[AMR][1000 genomes]
rs591094	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs630253	0.92[AMR][1000 genomes]
rs704973	0.94[AMR][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	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv1804804	chr3:42515186-42582403	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42528200-42535400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr3:42530200-42532200	Enhancers	Fetal Muscle Trunk	muscle
3	chr3:42530200-42532400	Enhancers	Gastric	stomach
4	chr3:42530200-42532600	Enhancers	Stomach Mucosa	stomach
5	chr3:42530200-42535200	Enhancers	Placenta	Placenta
6	chr3:42530200-42535600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr3:42530200-42535600	Enhancers	Lung	lung
8	chr3:42530400-42532400	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr3:42530800-42532200	Enhancers	Fetal Muscle Leg	muscle
10	chr3:42530800-42532600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:42530800-42532600	Enhancers	Pancreas	Pancrea
12	chr3:42530800-42532800	Enhancers	NHEK	skin
13	chr3:42530800-42535000	Enhancers	Primary B cells from cord blood	blood
14	chr3:42530800-42535000	Enhancers	Primary B cells from peripheral blood	blood
15	chr3:42531000-42532200	Enhancers	Stomach Smooth Muscle	stomach
16	chr3:42531000-42532200	Enhancers	Spleen	Spleen
17	chr3:42531000-42532400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr3:42531000-42532600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:42531000-42532600	Enhancers	Esophagus	oesophagus
20	chr3:42531000-42532600	Enhancers	Hela-S3	cervix
21	chr3:42531000-42532600	Enhancers	HMEC	breast
22	chr3:42531000-42532600	Enhancers	HSMMtube	muscle
23	chr3:42531000-42532800	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr3:42531000-42534400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:42531200-42532200	Enhancers	Duodenum Mucosa	Duodenum
26	chr3:42531200-42532200	Enhancers	Fetal Lung	lung
27	chr3:42531200-42532200	Enhancers	Right Atrium	heart
28	chr3:42531200-42532200	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr3:42531200-42532600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:42531200-42532600	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr3:42531200-42532600	Enhancers	Left Ventricle	heart
32	chr3:42531200-42532600	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr3:42531200-42532600	Enhancers	HUVEC	blood vessel
34	chr3:42531200-42532800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:42531400-42532200	Enhancers	Colon Smooth Muscle	Colon
36	chr3:42531400-42532400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr3:42531400-42532400	Flanking Active TSS	GM12878-XiMat	blood
38	chr3:42531400-42533600	Weak transcription	Adipose Nuclei	Adipose
39	chr3:42531600-42532000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:42531600-42532000	Enhancers	Right Ventricle	heart
41	chr3:42531600-42532200	Enhancers	H1 Cell Line	embryonic stem cell
42	chr3:42531600-42532200	Enhancers	HSMM	muscle
43	chr3:42531600-42532200	Enhancers	NH-A	brain
44	chr3:42531600-42532400	Enhancers	Aorta	Aorta
45	chr3:42531600-42532400	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr3:42531600-42532600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:42531600-42532600	Enhancers	A549	lung
48	chr3:42531800-42532000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:42531800-42532000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:42531800-42532200	Enhancers	H9 Cell Line	embryonic stem cell

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