Variant report

Variant	rs673560
Chromosome Location	chr3:42546860-42546861
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	chr3:42530093..42535343-chr3:42545492..42550064,6	MCF-7	breast:
3	chr3:42542139..42544178-chr3:42546531..42549362,2	K562	blood:
4	chr3:42543941..42547920-chr3:42554474..42558044,4	K562	blood:

Variant related genes	Relation type
ENSG00000114812	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1078008	0.90[EUR][1000 genomes]
rs182921	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs342542	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs399582	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs406683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs421558	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62248806	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv527430	chr3:42534042-42557199	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1814102	chr3:42539966-42582403	Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42544600-42548800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:42544600-42551600	Weak transcription	Pancreas	Pancrea
3	chr3:42544800-42548400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr3:42544800-42548600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:42544800-42548600	Weak transcription	Esophagus	oesophagus
6	chr3:42544800-42548800	Weak transcription	Left Ventricle	heart
7	chr3:42544800-42548800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:42544800-42550600	Weak transcription	Right Atrium	heart
9	chr3:42545000-42547400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:42545000-42547400	Weak transcription	Right Ventricle	heart
11	chr3:42545000-42547600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:42545000-42548600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:42545000-42548600	Weak transcription	Liver	Liver
14	chr3:42545000-42548800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:42545000-42549800	Weak transcription	Small Intestine	intestine
16	chr3:42545200-42547000	Active TSS	Lung	lung
17	chr3:42545200-42547000	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr3:42545200-42547600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr3:42545200-42548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:42545200-42548800	Weak transcription	NHEK	skin
21	chr3:42545400-42547400	Enhancers	Stomach Mucosa	stomach
22	chr3:42545400-42549000	Enhancers	Primary T cells from cord blood	blood
23	chr3:42545400-42551400	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr3:42545400-42553800	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr3:42545600-42547000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr3:42545600-42547200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:42545600-42548600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:42545600-42548600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:42545600-42548800	Weak transcription	Gastric	stomach
30	chr3:42545600-42550200	Enhancers	Primary T cells fromperipheralblood	blood
31	chr3:42545800-42547000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr3:42545800-42547400	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr3:42545800-42547400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:42545800-42547800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr3:42545800-42548400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr3:42545800-42548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:42545800-42549000	Weak transcription	Brain Angular Gyrus	brain
38	chr3:42545800-42549000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:42546000-42547800	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr3:42546000-42549400	Weak transcription	Brain Anterior Caudate	brain
41	chr3:42546200-42547000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:42546200-42548600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:42546200-42548600	Weak transcription	Fetal Heart	heart
44	chr3:42546200-42548600	Weak transcription	Placenta	Placenta
45	chr3:42546400-42547000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:42546400-42547000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr3:42546400-42547200	Flanking Active TSS	Fetal Intestine Large	intestine
48	chr3:42546400-42547800	Flanking Active TSS	Colonic Mucosa	Colon
49	chr3:42546400-42548000	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr3:42546600-42547000	Flanking Active TSS	Adipose Nuclei	Adipose

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