Variant report

Variant	rs413042
Chromosome Location	chr3:42560883-42560884
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:42560029..42560955-chr3:42577630..42578164,2	K562	blood:
2	chr3:42552045..42554738-chr3:42559579..42561082,2	K562	blood:
3	chr3:42556101..42557803-chr3:42559500..42561568,2	K562	blood:
4	chr3:42560470..42561419-chr3:42581081..42581582,2	K562	blood:
5	chr3:42546908..42549650-chr3:42559175..42561054,2	MCF-7	breast:
6	chr3:42559156..42562074-chr3:42562895..42565199,3	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SEC22C-1	chr3:42560881-42560944	ENSG00000232354.3

No data

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1511955	0.81[ASN][1000 genomes]
rs550431	0.81[ASN][1000 genomes]
rs55886057	0.81[ASN][1000 genomes]
rs6797853	0.85[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:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42547200-42561800	Genic enhancers	Fetal Intestine Small	intestine
2	chr3:42547600-42579000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:42549200-42561800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:42552200-42581000	Weak transcription	Pancreas	Pancrea
5	chr3:42552400-42570000	Weak transcription	Fetal Stomach	stomach
6	chr3:42553600-42566600	Weak transcription	Primary B cells from cord blood	blood
7	chr3:42557400-42566200	Weak transcription	Brain Anterior Caudate	brain
8	chr3:42557600-42569800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:42557600-42571600	Weak transcription	Brain Angular Gyrus	brain
10	chr3:42557600-42574000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:42557600-42574400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:42557800-42586000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:42557800-42590400	Weak transcription	Aorta	Aorta
14	chr3:42558000-42570200	Weak transcription	Adipose Nuclei	Adipose
15	chr3:42558000-42573000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:42558000-42585200	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:42558200-42561600	Weak transcription	Right Ventricle	heart
18	chr3:42558400-42561000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:42558400-42561000	Weak transcription	NHEK	skin
20	chr3:42558800-42561200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:42558800-42561600	Weak transcription	Right Atrium	heart
22	chr3:42558800-42562400	Weak transcription	Left Ventricle	heart
23	chr3:42559200-42561600	Weak transcription	Esophagus	oesophagus
24	chr3:42559200-42561600	Weak transcription	Spleen	Spleen
25	chr3:42559200-42561800	Weak transcription	Fetal Heart	heart
26	chr3:42559600-42561400	Genic enhancers	Duodenum Mucosa	Duodenum
27	chr3:42560200-42561200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
28	chr3:42560200-42561600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:42560200-42561600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr3:42560200-42562400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr3:42560200-42562600	Genic enhancers	Lung	lung
32	chr3:42560200-42563000	Genic enhancers	Monocytes-CD14+_RO01746	blood
33	chr3:42560200-42573400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:42560400-42561400	Enhancers	Primary T cells fromperipheralblood	blood
35	chr3:42560400-42561600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:42560400-42561800	Genic enhancers	Fetal Intestine Large	intestine
37	chr3:42560400-42562200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:42560400-42562400	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr3:42560400-42562600	Enhancers	Stomach Mucosa	stomach
40	chr3:42560400-42562800	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr3:42560400-42562800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr3:42560400-42562800	Genic enhancers	Rectal Mucosa Donor 29	rectum
43	chr3:42560400-42563400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:42560600-42561000	Enhancers	Gastric	stomach
45	chr3:42560600-42562400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:42560600-42562800	Genic enhancers	Rectal Mucosa Donor 31	rectum
47	chr3:42560600-42563000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:42560600-42563200	Genic enhancers	Primary monocytes fromperipheralblood	blood
49	chr3:42560800-42561000	Genic enhancers	Colonic Mucosa	Colon
50	chr3:42560800-42561600	Genic enhancers	Primary T cells from cord blood	blood

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