Variant report

Variant	nsv823400
Chromosome Location	chr6:1612778-1613621
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:18)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:2)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:1613541..1614425-chr6:1641560..1642119,3	MCF-7	breast:
2	chr6:1612565..1615275-chr6:1837590..1839107,2	MCF-7	breast:
3	chr1:183441719..183444081-chr6:1612481..1614965,2	MCF-7	breast:
4	chr6:1611214..1613001-chr6:2041317..2043810,2	MCF-7	breast:
5	chr6:1612605..1614594-chr6:1617750..1620318,2	K562	blood:
6	chr6:1612494..1615565-chr6:2103145..2107069,5	MCF-7	breast:
7	chr6:1613601..1616757-chr6:1636130..1638960,3	MCF-7	breast:
8	chr6:1611913..1614321-chr6:1833472..1836057,3	MCF-7	breast:
9	chr6:1610715..1613985-chr6:2196585..2199138,3	MCF-7	breast:
10	chr6:1612951..1615735-chr6:3066934..3068619,2	MCF-7	breast:
11	chr6:1613541..1614598-chr6:1641560..1642153,3	MCF-7	breast:
12	chr6:1612762..1614490-chr6:1684651..1686337,2	MCF-7	breast:
13	chr6:1613450..1614402-chr6:1641238..1641879,5	MCF-7	breast:
14	chr6:1607121..1609914-chr6:1613223..1615033,2	K562	blood:
15	chr6:1612582..1614145-chr6:1846859..1849142,2	MCF-7	breast:
16	chr6:1613523..1614289-chr6:1838606..1839498,2	MCF-7	breast:
17	chr6:1612577..1614591-chr6:1838798..1840944,2	MCF-7	breast:
18	chr6:1612642..1614747-chr6:1828037..1830665,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXC1-3	chr6:1612577-1614127	NONHSAT106538

No data

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

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	FOXC1	hsa-miR-204-5p	chr6:1612948-1612968
2	FOXC1	hsa-miR-204-5p	chr6:1612961-1612968

Variant related genes	Relation type
ENSG00000116698	chromatin interactions
ENSG00000112699	chromatin interactions

Extended variants
information (count: 30 )
Associated
traits (count: 71 )

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs533280855	chr6:1612813-1612814	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
2	rs547974202	chr6:1612827-1612828	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
3	rs77607008	chr6:1612889-1612890	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
4	rs34877245	chr6:1612918-1612919	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs528961345	chr6:1612981-1612982	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
6	rs549100468	chr6:1612984-1612985	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
7	rs373198124	chr6:1613037-1613038	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs565331544	chr6:1613057-1613058	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs35717904	chr6:1613076-1613077	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs550980014	chr6:1613128-1613129	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs533511348	chr6:1613162-1613163	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs571583124	chr6:1613163-1613164	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
13	rs537378863	chr6:1613176-1613177	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
14	rs377765731	chr6:1613187-1613188	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
15	rs557259848	chr6:1613202-1613203	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs35607877	chr6:1613245-1613246	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs574217067	chr6:1613269-1613270	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
18	rs549895092	chr6:1613300-1613301	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
19	rs560601928	chr6:1613338-1613339	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
20	rs140591342	chr6:1613361-1613362	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs371193842	chr6:1613381-1613382	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
22	rs573385129	chr6:1613398-1613399	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
23	rs545386506	chr6:1613409-1613410	Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
24	rs190526847	chr6:1613434-1613435	Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
25	rs529818974	chr6:1613455-1613456	Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
26	rs984253	chr6:1613529-1613530	Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs182014366	chr6:1613540-1613541	Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
28	rs34470720	chr6:1613570-1613571	Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs35347817	chr6:1613593-1613594	Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
30	rs529133151	chr6:1613594-1613595	Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:71)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Myelofibrosis	22110671	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Prader-willi syndrome	20588305	CNVD
Multiple myeloma	16616336	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Developmental delay	19490664	CNVD
Cancer	21183584	CNVD
Multiple Epiphyseal Dysplasia	20877625	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Glaucoma	18694899	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Prostate cancer	16573809	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	17603634	CNVD
Cancer	20164920	CNVD
Colorectal cancer	21297112	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Follicular lymphoma	20505157	CNVD
Glioblastoma multiforme	21080181	CNVD
Ewing''s sarcoma	21437220	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Leukemia	21518781	CNVD
Cancer	21637783	CNVD
Facial dysmorphism	22105932	CNVD
Medulloblastoma	21979893	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Hepatocellular carcinoma	22174799	CNVD
Endometrial cancer	22040021	CNVD
Acute myeloid leukemia	16864856	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Bladder cancer	19088036	CNVD
Wilms tumour	21544195	CNVD
Uveal melanoma	21693616	CNVD
Biliary cancer	19435499	CNVD
Malaria	21533027	CNVD
Retinoblastoma	19183342	CNVD
Acute myeloid leukemia	20729466	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Prostate cancer	18632612	CNVD
Myelodysplastic syndrome	21251322	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Breast cancer	21858162	CNVD
Breast cancer	21364760	CNVD
Lung cancer	18438408	CNVD
Bladder cancer	21909424	CNVD
Multiple myeloma	17550852	CNVD
Ewing''s sarcoma	17952124	CNVD
Cancer	20164919	CNVD
Gastric cancer	16891809	CNVD
Ovarian cancer	21781307	CNVD
small cell lung cancer	20016488	CNVD
Autism	22495311	CNVD
Autism	21448237	CNVD
Lung adenocarcinoma	21935476	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:135 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1605600-1620800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:1609000-1615200	Active TSS	Right Atrium	heart
3	chr6:1609000-1615400	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr6:1609200-1612800	Active TSS	HSMM	muscle
5	chr6:1609200-1614400	Active TSS	A549	lung
6	chr6:1609400-1616000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:1609600-1614400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:1609600-1614800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:1609600-1616000	Active TSS	Hela-S3	cervix
10	chr6:1609800-1613800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:1609800-1613800	Active TSS	HUVEC	blood vessel
12	chr6:1609800-1614000	Active TSS	NHLF	lung
13	chr6:1609800-1614600	Active TSS	HMEC	breast
14	chr6:1610400-1614000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:1610800-1612800	Transcr. at gene 5' and 3'	Aorta	Aorta
16	chr6:1611000-1615400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:1611200-1613200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
18	chr6:1611200-1614000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
19	chr6:1611200-1614600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:1611200-1615600	Bivalent/Poised TSS	Left Ventricle	heart
21	chr6:1611600-1612800	Bivalent/Poised TSS	Esophagus	oesophagus
22	chr6:1611800-1612800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
23	chr6:1612000-1612800	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:1612000-1612800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:1612000-1612800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
26	chr6:1612000-1612800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
27	chr6:1612000-1612800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
28	chr6:1612000-1612800	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:1612000-1613000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
30	chr6:1612000-1613400	Bivalent/Poised TSS	Brain Substantia Nigra	brain
31	chr6:1612000-1613600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:1612000-1615400	Bivalent/Poised TSS	NH-A	brain
33	chr6:1612200-1612800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
34	chr6:1612200-1612800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
35	chr6:1612200-1612800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
36	chr6:1612200-1612800	Flanking Bivalent TSS/Enh	Placenta	Placenta
37	chr6:1612200-1612800	Flanking Bivalent TSS/Enh	Rectal Smooth Muscle	rectum
38	chr6:1612200-1612800	Enhancers	Dnd41	blood
39	chr6:1612200-1612800	Flanking Bivalent TSS/Enh	HepG2	liver
40	chr6:1612200-1613000	Transcr. at gene 5' and 3'	Osteobl	bone
41	chr6:1612200-1613200	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
42	chr6:1612200-1613800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:1612200-1614000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:1612200-1614200	Bivalent/Poised TSS	Fetal Kidney	kidney
45	chr6:1612200-1614200	Weak transcription	Spleen	Spleen
46	chr6:1612200-1614200	Bivalent/Poised TSS	NHDF-Ad	bronchial
47	chr6:1612200-1615400	Bivalent/Poised TSS	Psoas Muscle	Psoas
48	chr6:1612200-1616200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr6:1612200-1617000	Bivalent/Poised TSS	Brain Anterior Caudate	brain
50	chr6:1612400-1612800	Bivalent Enhancer	H9 Cell Line	embryonic stem cell

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