Variant report

Variant	esv3348972
Chromosome Location	chr1:209945126-209945450
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:47)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:47 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:209945272-209945317	GM12891	blood:	n/a	n/a
2	CTCF	chr1:209945179-209945244	MCF-7	breast:	n/a	n/a
3	CTCF	chr1:209943655-209945439	GM19239	blood:	n/a	n/a
4	CTCF	chr1:209945214-209945314	GM10266	blood:	n/a	n/a
5	CTCF	chr1:209945261-209945329	MCF-7	breast:	n/a	n/a
6	CTCF	chr1:209945138-209945254	GM12891	blood:	n/a	n/a
7	CTCF	chr1:209945318-209945338	NHEK	skin:	n/a	n/a
8	GATA2	chr1:209945406-209945911	SH-SY5Y	brain:	n/a	n/a
9	GATA3	chr1:209945412-209945809	SH-SY5Y	brain:	n/a	n/a
10	IRF4	chr1:209944855-209945464	GM12878	blood:	n/a	n/a
11	MYC	chr1:209945086-209945222	MCF-7	breast:	n/a	n/a
12	MYC	chr1:209945227-209945234	MCF-7	breast:	n/a	n/a
13	MYC	chr1:209945106-209945200	MCF-7	breast:	n/a	n/a
14	MYC	chr1:209944955-209945349	MCF-7	breast:	n/a	n/a
15	MYC	chr1:209945226-209945323	MCF-7	breast:	n/a	n/a
16	MYC	chr1:209945022-209945352	MCF-7	breast:	n/a	n/a
17	PAX5	chr1:209945056-209945441	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:209945143-209945225	MCF-7	breast:	n/a	n/a
19	POLR2A	chr1:209941560-209945629	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:209944289-209945552	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:209942360-209945616	GM12892	blood:	n/a	n/a
22	POLR2A	chr1:209943573-209945492	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:209941520-209945190	GM15510	blood:	n/a	n/a
24	POLR2A	chr1:209944809-209945362	Gliobla	brain:	n/a	n/a
25	POLR2A	chr1:209943578-209945455	GM12891	blood:	n/a	n/a
26	POLR2A	chr1:209945003-209945443	GM12891	blood:	n/a	n/a
27	POLR2A	chr1:209945131-209945335	K562	blood:	n/a	n/a
28	POLR2A	chr1:209941509-209947286	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:209941568-209945214	GM18951	blood:	n/a	n/a
30	POLR2A	chr1:209943512-209945521	GM12891	blood:	n/a	n/a
31	POLR2A	chr1:209941597-209945746	GM19099	blood:	n/a	n/a
32	POLR2A	chr1:209940700-209952492	GM12891	blood:	n/a	n/a
33	POLR2A	chr1:209943517-209945479	GM12892	blood:	n/a	n/a
34	POLR2A	chr1:209944836-209945332	A549	lung:	n/a	n/a
35	POLR2A	chr1:209943536-209945521	GM12891	blood:	n/a	n/a
36	POLR2A	chr1:209944334-209945446	MCF-7	breast:	n/a	n/a
37	POLR2A	chr1:209941117-209946709	GM18505	blood:	n/a	n/a
38	POLR2A	chr1:209942381-209945631	GM12892	blood:	n/a	n/a
39	POLR2A	chr1:209942422-209945671	GM12892	blood:	n/a	n/a
40	POLR2A	chr1:209945305-209945505	GM12878	blood:	n/a	n/a
41	POLR2A	chr1:209943616-209945450	GM12878	blood:	n/a	n/a
42	POU2F2	chr1:209944667-209945455	GM12891	blood:	n/a	n/a
43	POU2F2	chr1:209944640-209945550	GM12891	blood:	n/a	n/a
44	POU2F2	chr1:209944894-209945487	GM12878	blood:	n/a	n/a
45	STAT5A	chr1:209942515-209946308	GM12878	blood:	n/a	chr1:209942981-209942989 chr1:209942982-209942994 chr1:209945841-209945853 chr1:209943537-209943545
46	STAT5A	chr1:209945242-209945548	GM12878	blood:	n/a	n/a
47	ZEB1	chr1:209943163-209945525	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209944533..209945329-chr11:75062797..75063297,2	NB4	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf74-2	chr1:209944455-209945468	NONHSAT009239
2	lnc-HSD11B1-4	chr1:209944247-209945468	NONHSAT009240
3	lnc-HSD11B1-4	chr1:209944860-209945499	NONHSAT009242
4	lnc-HSD11B1-4	chr1:209944247-209945468	NONHSAT009238
5	lnc-HSD11B1-4	chr1:209944790-209945471	NONHSAT009237
6	lnc-HSD11B1-4	chr1:209945420-209945499	NONHSAT009236

No data

Variant related genes	Relation type
TRAF3IP3	TF binding region
ENSG00000137486	chromatin interactions

Extended variants
information (count: 24 )
Associated
traits (count: 89 )

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs28767240	chr1:209945129-209945130	Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs536338511	chr1:209945145-209945146	Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
3	rs187186172	chr1:209945179-209945180	Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
4	rs373537716	chr1:209945205-209945206	Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
5	rs576317817	chr1:209945206-209945207	Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
6	rs554595017	chr1:209945212-209945213	Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
7	rs369067106	chr1:209945219-209945220	Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
8	rs373023798	chr1:209945225-209945226	Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
9	rs367761607	chr1:209945231-209945232	Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
10	rs534483420	chr1:209945234-209945235	Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
11	rs553153563	chr1:209945235-209945236	Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
12	rs113900634	chr1:209945236-209945237	Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
13	rs377340358	chr1:209945239-209945240	Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
14	rs545318207	chr1:209945248-209945249	Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
15	rs58558913	chr1:209945250-209945251	Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
16	rs397949802	chr1:209945251-209945252	Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
17	rs563262276	chr1:209945297-209945298	Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
18	rs575355460	chr1:209945298-209945299	Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
19	rs111321155	chr1:209945343-209945344	Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
20	rs371453007	chr1:209945369-209945370	Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs200058437	chr1:209945420-209945421	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Strong transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
22	rs201689173	chr1:209945427-209945428	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Strong transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
23	rs191566151	chr1:209945428-209945429	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Strong transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
24	rs183713561	chr1:209945430-209945431	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Strong transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:89)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Liposarcoma	21253554	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Medulloblastoma	21979893	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Neuroblastoma	21899760	CNVD
Glioblastoma multiforme	17002787	CNVD
Breast cancer	21858162	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	21611746	CNVD
Breast cancer	17393978	CNVD
Hepatocellular carcinoma	16750200	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Trisomy 5 syndrome	21098271	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	CNVD
Macular degeneration	22558131	CNVD
Alzheimer''s disease	21403675	CNVD
Multiple myeloma	16461302	CNVD
van der Woude syndrome	22470819	CNVD
van der Woude syndrome	20818247	CNVD
T-cell lymphomas	19863542	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	17060936	CNVD
Atypical hemolytic uremic syndrome	19861685	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	21364760	CNVD
small cell lung cancer	20016488	CNVD
Ovarian clear cell carcinoma	19293255	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209940800-209946200	Enhancers	Fetal Stomach	stomach
2	chr1:209941000-209945800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:209942000-209945400	Enhancers	Placenta	Placenta
4	chr1:209942800-209956800	Weak transcription	Small Intestine	intestine
5	chr1:209942800-209957200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:209943200-209945400	Enhancers	Lung	lung
7	chr1:209943200-209945600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr1:209943200-209950600	Weak transcription	Psoas Muscle	Psoas
9	chr1:209943400-209945400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr1:209943400-209952600	Weak transcription	Fetal Intestine Small	intestine
11	chr1:209943600-209945600	Enhancers	Primary hematopoietic stem cells	blood
12	chr1:209943600-209945600	Enhancers	Gastric	stomach
13	chr1:209943600-209945800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr1:209943600-209951000	Weak transcription	HSMMtube	muscle
15	chr1:209943600-209956600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:209943800-209945400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:209943800-209945600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
18	chr1:209943800-209945600	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr1:209943800-209950800	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:209943800-209954600	Weak transcription	NHEK	skin
21	chr1:209943800-209956600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:209943800-209956600	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:209943800-209957000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:209943800-209957200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:209944000-209945800	Enhancers	Fetal Heart	heart
26	chr1:209944000-209946000	Enhancers	Stomach Smooth Muscle	stomach
27	chr1:209944000-209946200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:209944000-209952800	Weak transcription	HMEC	breast
29	chr1:209944000-209956000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:209944000-209956600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:209944200-209945200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:209944200-209945200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:209944200-209945800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:209944200-209946400	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
35	chr1:209944400-209945800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr1:209944400-209947200	Weak transcription	Right Atrium	heart
37	chr1:209944400-209948800	Genic enhancers	Monocytes-CD14+_RO01746	blood
38	chr1:209944600-209945200	Enhancers	Pancreas	Pancrea
39	chr1:209944600-209946000	Genic enhancers	Fetal Thymus	thymus
40	chr1:209944600-209946400	Genic enhancers	Thymus	Thymus
41	chr1:209944600-209954400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr1:209944800-209945200	Active TSS	Colonic Mucosa	Colon
43	chr1:209944800-209945400	Weak transcription	K562	blood
44	chr1:209944800-209946000	Genic enhancers	Primary monocytes fromperipheralblood	blood
45	chr1:209944800-209946200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
46	chr1:209944800-209947800	Genic enhancers	Primary B cells from cord blood	blood
47	chr1:209944800-209950000	Genic enhancers	Primary B cells from peripheral blood	blood
48	chr1:209944800-209951200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:209944800-209955200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:209944800-209956600	Weak transcription	Brain Inferior Temporal Lobe	brain

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