Variant report

Variant	rs580447
Chromosome Location	chr3:42565674-42565675
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:42564995-42567233	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42564213..42566544-chr3:42567890..42569436,2	K562	blood:

Variant related genes	Relation type
VIPR1	TF binding region
ENSG00000114812	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10154957	1.00[AMR][1000 genomes]
rs13320598	1.00[AMR][1000 genomes]
rs13325536	1.00[AMR][1000 genomes]
rs1511955	0.84[ASN][1000 genomes]
rs28508060	1.00[AMR][1000 genomes]
rs28549046	1.00[AMR][1000 genomes]
rs472663	1.00[ASN][1000 genomes]
rs550431	0.84[ASN][1000 genomes]
rs55886057	0.84[ASN][1000 genomes]
rs58273990	1.00[AMR][1000 genomes]
rs9812538	1.00[AMR][1000 genomes]
rs9812673	1.00[AMR][1000 genomes]
rs9822273	1.00[AMR][1000 genomes]
rs9832720	1.00[AMR][1000 genomes]
rs9841926	1.00[AMR][1000 genomes]
rs9853946	1.00[AMR][1000 genomes]
rs9855071	1.00[AMR][1000 genomes]
rs9869491	1.00[AMR][1000 genomes]
rs9876937	1.00[AMR][1000 genomes]
rs9884030	1.00[AMR][1000 genomes]
rs9985232	1.00[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	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
5	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

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42547600-42579000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:42552200-42581000	Weak transcription	Pancreas	Pancrea
3	chr3:42552400-42570000	Weak transcription	Fetal Stomach	stomach
4	chr3:42553600-42566600	Weak transcription	Primary B cells from cord blood	blood
5	chr3:42557400-42566200	Weak transcription	Brain Anterior Caudate	brain
6	chr3:42557600-42569800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:42557600-42571600	Weak transcription	Brain Angular Gyrus	brain
8	chr3:42557600-42574000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:42557600-42574400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:42557800-42586000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:42557800-42590400	Weak transcription	Aorta	Aorta
12	chr3:42558000-42570200	Weak transcription	Adipose Nuclei	Adipose
13	chr3:42558000-42573000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:42558000-42585200	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:42560200-42573400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:42561000-42581000	Weak transcription	Gastric	stomach
17	chr3:42561400-42570400	Strong transcription	Duodenum Mucosa	Duodenum
18	chr3:42561800-42568600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:42562000-42567600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:42562200-42566600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:42562400-42566600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:42562400-42567000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr3:42562400-42567600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr3:42562400-42570800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:42562400-42586800	Weak transcription	Small Intestine	intestine
26	chr3:42562600-42566000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:42562600-42566600	Weak transcription	Esophagus	oesophagus
28	chr3:42562600-42567000	Weak transcription	Placenta	Placenta
29	chr3:42562800-42565800	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr3:42562800-42567200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr3:42562800-42574200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:42563000-42566000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:42563000-42566200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:42563000-42566600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:42563000-42572400	Weak transcription	Right Ventricle	heart
36	chr3:42563200-42565800	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr3:42563600-42575000	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr3:42564000-42577400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr3:42564400-42566400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:42564400-42566600	Weak transcription	Liver	Liver
41	chr3:42564400-42570600	Genic enhancers	Lung	lung
42	chr3:42564600-42566400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:42564800-42565800	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr3:42564800-42565800	Weak transcription	Colonic Mucosa	Colon
45	chr3:42564800-42566400	Strong transcription	Fetal Intestine Small	intestine
46	chr3:42564800-42566600	Weak transcription	Fetal Intestine Large	intestine
47	chr3:42565000-42567000	Weak transcription	Primary T cells from cord blood	blood
48	chr3:42565000-42567200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:42565200-42566400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:42565200-42576400	Enhancers	Spleen	Spleen

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