Variant report

Variant	esv3421675
Chromosome Location	chr19:55943765-55946313
allele	n/a
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:8)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55917469..55921438-chr19:55945356..55952187,11	K562	blood:
2	chr19:55917487..55920420-chr19:55941767..55946909,5	MCF-7	breast:
3	chr19:55934645..55937575-chr19:55940137..55944163,4	K562	blood:
4	chr19:55917961..55920276-chr19:55940562..55944093,4	K562	blood:
5	chr19:55942273..55945441-chr19:55953460..55955338,3	K562	blood:
6	chr19:55915970..55920672-chr19:55938294..55944595,9	K562	blood:
7	chr19:55901062..55903652-chr19:55943271..55945381,2	K562	blood:
8	chr19:55941660..55944009-chr19:55947718..55950362,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ISOC2-3	chr19:55945844-55946911	NONHSAT068037
2	lnc-ISOC2-3	chr19:55945594-55945642	NONHSAT068037

No data

Variant related genes	Relation type
ENSG00000108106	chromatin interactions
ENSG00000187902	chromatin interactions

Extended variants
information (count: 130 )
Associated
traits (count: 70 )

Variant overlapped rSNPs/rCNVs (count:130 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs116236774	chr19:55943819-55943820	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs139712863	chr19:55943835-55943836	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs565765442	chr19:55943863-55943864	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs547279934	chr19:55943874-55943875	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs560240238	chr19:55943913-55943914	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs532368724	chr19:55943916-55943917	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs142610736	chr19:55943917-55943918	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs73606259	chr19:55943940-55943941	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs565539961	chr19:55943963-55943964	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs573117812	chr19:55944012-55944013	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs550471894	chr19:55944016-55944017	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs567466643	chr19:55944021-55944022	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs536112459	chr19:55944112-55944113	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs553231170	chr19:55944116-55944117	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs112959251	chr19:55944121-55944122	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs79292503	chr19:55944125-55944126	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs117713780	chr19:55944129-55944130	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs77548043	chr19:55944166-55944167	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs575383801	chr19:55944195-55944196	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs551921760	chr19:55944264-55944265	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs544341474	chr19:55944296-55944297	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs561285922	chr19:55944340-55944341	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs62128227	chr19:55944363-55944364	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs540516757	chr19:55944373-55944374	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs544373186	chr19:55944455-55944456	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs528310702	chr19:55944497-55944498	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs192638502	chr19:55944512-55944513	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs562610416	chr19:55944665-55944666	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs532701898	chr19:55944683-55944684	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs552128696	chr19:55944708-55944709	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs28569041	chr19:55944816-55944817	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs375494849	chr19:55944876-55944877	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs562562295	chr19:55944885-55944886	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs531656729	chr19:55945025-55945026	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs368885389	chr19:55945026-55945027	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs202168345	chr19:55945061-55945062	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs548198173	chr19:55945072-55945073	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs548670002	chr19:55945123-55945124	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs114502587	chr19:55945218-55945219	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs529891631	chr19:55945250-55945251	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs559880465	chr19:55945253-55945254	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs546514068	chr19:55945277-55945278	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs566754468	chr19:55945291-55945292	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs185075664	chr19:55945316-55945317	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs189030981	chr19:55945324-55945325	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs201829253	chr19:55945365-55945366	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs73606260	chr19:55945368-55945369	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs199988348	chr19:55945371-55945372	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs200867422	chr19:55945372-55945373	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs386811069	chr19:55945373-55945374	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:70)

Disease	PMID	Source
Myelodysplastic syndrome	17634407	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Cancer	21637783	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Ovarian cancer	21720365	CNVD
Cancer	20164919	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Ductal carcinoma	22052326	CNVD
Congenital nephrotic syndrome	18421352	CNVD
Astrocytoma	17934521	CNVD
Leukemia	17361228	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Breast cancer	17603634	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Endometrial cancer	22040021	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Oligodendroglial tumors	17285580	CNVD
renal disease	20603712	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Acute myeloid leukemia	20729466	CNVD
Ovarian cancer	22174824	CNVD
Multiple myeloma	16616336	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Wilms tumour	21544195	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Congenital anomalies of the kidney and urinary tract	18852474	CNVD
Glioblastoma multiforme	17002787	CNVD
Cervical cancer	21062161	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Prostate cancer	16573809	CNVD
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Lung cancer	18438408	CNVD
Colorectal cancer	16272173	CNVD
Ovarian cancer	21781307	CNVD
Neuroblastoma	20406844	CNVD
Breast cancer	21785460	CNVD
Breast cancer	20459607	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Lung adenocarcinoma	17086460	CNVD
Lung cancer	17086460	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Myelofibrosis	22110671	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Alzheimer''s disease	22166940	CNVD
Heart disease	21282601	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Glioblastoma multiforme	21922591	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Breast cancer	21509527	CNVD

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55941200-55944400	Strong transcription	Brain Hippocampus Middle	brain
2	chr19:55941200-55953400	Weak transcription	Right Atrium	heart
3	chr19:55941400-55944600	Strong transcription	Brain Inferior Temporal Lobe	brain
4	chr19:55941600-55944200	Strong transcription	Brain Angular Gyrus	brain
5	chr19:55941600-55946800	Strong transcription	Brain Cingulate Gyrus	brain
6	chr19:55942200-55943800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr19:55942600-55945000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr19:55943000-55945800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr19:55943800-55944000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
10	chr19:55943800-55944600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:55943800-55945600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:55944000-55944200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
13	chr19:55944200-55944400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
14	chr19:55944200-55944400	Enhancers	Pancreas	Pancrea
15	chr19:55944200-55952400	Weak transcription	Brain Angular Gyrus	brain
16	chr19:55944400-55944600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr19:55944400-55944600	Bivalent Enhancer	Brain Hippocampus Middle	brain
18	chr19:55944400-55944600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr19:55944400-55944600	Bivalent Enhancer	Fetal Muscle Leg	muscle
20	chr19:55944400-55944600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
21	chr19:55944400-55945200	Weak transcription	Pancreas	Pancrea
22	chr19:55944600-55944800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:55944600-55945000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr19:55944600-55945400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr19:55944600-55945800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr19:55944800-55945000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:55944800-55945000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
28	chr19:55945000-55945200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:55945000-55945200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr19:55945200-55945400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
31	chr19:55945200-55945400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:55945200-55945400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
33	chr19:55945200-55945400	Bivalent Enhancer	Fetal Muscle Leg	muscle
34	chr19:55945200-55945800	Enhancers	Gastric	stomach
35	chr19:55945200-55945800	Enhancers	Pancreas	Pancrea
36	chr19:55945200-55948200	Weak transcription	Brain Hippocampus Middle	brain
37	chr19:55945400-55947000	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr19:55945600-55945800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr19:55945600-55945800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr19:55945600-55945800	Bivalent/Poised TSS	Fetal Kidney	kidney
41	chr19:55945600-55946600	Bivalent Enhancer	Esophagus	oesophagus
42	chr19:55945600-55946800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr19:55945800-55946000	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
44	chr19:55945800-55946000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr19:55945800-55946000	ZNF genes & repeats	Fetal Kidney	kidney
46	chr19:55945800-55946000	Bivalent Enhancer	Gastric	stomach
47	chr19:55945800-55946200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr19:55945800-55946200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
49	chr19:55945800-55946600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:55945800-55946600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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