Variant report

Variant	rs55848952
Chromosome Location	chr4:1388419-1388420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NKX1-1-1	chr4:1388324-1388811	NONHSAT094711

Extended variants
information (count: 31 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv878328	chr4:1141573-1990425	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
5	nsv878330	chr4:1147407-1523930	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
6	nsv461152	chr4:1159680-1415698	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	nsv593278	chr4:1159680-1415698	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
8	nsv997971	chr4:1191256-1518521	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
9	nsv878341	chr4:1277826-1391400	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv1002635	chr4:1282603-1402761	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv878343	chr4:1291337-1391400	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
12	nsv878344	chr4:1291337-1414684	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv878345	chr4:1291337-1563920	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
14	nsv878347	chr4:1300077-1866358	Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
15	esv1794294	chr4:1307119-1817474	Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
16	nsv878350	chr4:1320023-1500753	Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
17	nsv878351	chr4:1329847-1414684	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
18	nsv1008785	chr4:1335089-1518521	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
19	nsv536988	chr4:1335089-1518521	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
20	nsv593302	chr4:1338618-1414684	ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
21	esv1826930	chr4:1373206-1399091	Bivalent Enhancer Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
22	esv1851616	chr4:1373206-1399091	Bivalent Enhancer ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
23	nsv870062	chr4:1376068-1523451	Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
24	nsv1003107	chr4:1380178-1710751	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
25	nsv1005964	chr4:1380178-1949459	Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
26	esv1805446	chr4:1386570-1391550	Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
27	esv1817437	chr4:1386570-1391550	ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
28	esv3406646	chr4:1387377-1389925	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
29	esv3403340	chr4:1387777-1390325	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
30	esv14957	chr4:1387978-1392638	ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
31	esv11309	chr4:1388033-1389448	Weak transcription Strong transcription ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1341800-1388800	Weak transcription	Small Intestine	intestine
2	chr4:1346000-1389200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr4:1360800-1389600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr4:1368800-1389200	Weak transcription	NHDF-Ad	bronchial
5	chr4:1378400-1390400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr4:1378600-1389200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr4:1380200-1388800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:1380400-1390200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:1380400-1391000	Weak transcription	Right Ventricle	heart
10	chr4:1380400-1391200	Weak transcription	Colon Smooth Muscle	Colon
11	chr4:1380400-1391400	Weak transcription	HepG2	liver
12	chr4:1380600-1390200	Weak transcription	Colonic Mucosa	Colon
13	chr4:1381400-1388800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:1382200-1392200	Weak transcription	Psoas Muscle	Psoas
15	chr4:1382600-1389800	Weak transcription	HSMM	muscle
16	chr4:1382600-1390400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr4:1382800-1388600	Weak transcription	HSMMtube	muscle
18	chr4:1382800-1390000	Weak transcription	NHEK	skin
19	chr4:1382800-1390200	Weak transcription	Osteobl	bone
20	chr4:1382800-1391200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:1384400-1391200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
22	chr4:1384800-1389600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:1385000-1388600	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr4:1385200-1389600	Strong transcription	Stomach Smooth Muscle	stomach
25	chr4:1385400-1388600	ZNF genes & repeats	Adipose Nuclei	Adipose
26	chr4:1385600-1390000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:1385800-1389800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:1386000-1388600	ZNF genes & repeats	Brain Germinal Matrix	brain
29	chr4:1386000-1391000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
30	chr4:1386200-1388800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:1386200-1389000	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr4:1386200-1389200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:1386200-1389400	ZNF genes & repeats	Esophagus	oesophagus
34	chr4:1386200-1389600	ZNF genes & repeats	Fetal Intestine Small	intestine
35	chr4:1386200-1389800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:1386200-1390600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr4:1386400-1389000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
38	chr4:1386400-1389600	Strong transcription	Brain Hippocampus Middle	brain
39	chr4:1386400-1389600	ZNF genes & repeats	Lung	lung
40	chr4:1386400-1391000	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr4:1386400-1391200	ZNF genes & repeats	Fetal Stomach	stomach
42	chr4:1386600-1388600	ZNF genes & repeats	Fetal Lung	lung
43	chr4:1386600-1388800	ZNF genes & repeats	Fetal Intestine Large	intestine
44	chr4:1386600-1389400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:1386600-1389400	Strong transcription	Primary T cells from cord blood	blood
46	chr4:1386600-1389600	ZNF genes & repeats	Spleen	Spleen
47	chr4:1386800-1389200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:1386800-1389400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr4:1386800-1389400	ZNF genes & repeats	Thymus	Thymus
50	chr4:1386800-1389800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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