Variant report

Variant	rs41289576
Chromosome Location	chr3:42572528-42572529
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SEC22C-1	chr3:42572352-42572544	ENSG00000232354.3

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

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs342515	1.00[ASN][1000 genomes]
rs55940287	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797853	1.00[ASN][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:52 , 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	chr3:42557600-42574000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:42557600-42574400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:42557800-42586000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:42557800-42590400	Weak transcription	Aorta	Aorta
7	chr3:42558000-42573000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:42558000-42585200	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:42560200-42573400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:42561000-42581000	Weak transcription	Gastric	stomach
11	chr3:42562400-42586800	Weak transcription	Small Intestine	intestine
12	chr3:42562800-42574200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:42563600-42575000	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr3:42564000-42577400	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr3:42565200-42576400	Enhancers	Spleen	Spleen
16	chr3:42567200-42573000	Weak transcription	Esophagus	oesophagus
17	chr3:42567600-42573800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr3:42567600-42580200	Strong transcription	Fetal Intestine Small	intestine
19	chr3:42567800-42572600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:42567800-42577200	Strong transcription	Fetal Intestine Large	intestine
21	chr3:42568000-42573000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr3:42568200-42573800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:42570000-42573200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:42570000-42580800	Weak transcription	Colonic Mucosa	Colon
25	chr3:42570200-42573000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:42570200-42573400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:42570800-42574800	Strong transcription	Duodenum Mucosa	Duodenum
28	chr3:42571200-42581200	Weak transcription	Right Atrium	heart
29	chr3:42571600-42574400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr3:42571600-42576600	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:42571800-42572600	Weak transcription	Brain Anterior Caudate	brain
32	chr3:42571800-42573000	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr3:42571800-42573800	Weak transcription	Adipose Nuclei	Adipose
34	chr3:42571800-42574000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:42571800-42576200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:42571800-42581600	Weak transcription	Liver	Liver
37	chr3:42571800-42586200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:42572000-42572800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr3:42572000-42573200	Weak transcription	Stomach Mucosa	stomach
40	chr3:42572000-42574600	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr3:42572000-42574600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:42572000-42575800	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr3:42572000-42576400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:42572200-42572600	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
45	chr3:42572200-42575600	Genic enhancers	Lung	lung
46	chr3:42572200-42576000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chr3:42572400-42572600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:42572400-42572800	Genic enhancers	Primary T cells fromperipheralblood	blood
49	chr3:42572400-42572800	Enhancers	Right Ventricle	heart
50	chr3:42572400-42573400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

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