Variant report

Variant	esv3501396
Chromosome Location	chr10:54068737-54069185
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr10:54068055-54068746	H1-hESC	embryonic stem cell:	n/a	chr10:54068152-54068162
2	CREB1	chr10:54068461-54068745	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr10:54068800-54068950	AG09309	skin:	n/a	n/a
4	CTCF	chr10:54067626-54068765	A549	lung:	n/a	chr10:54068119-54068132 chr10:54068119-54068128 chr10:54068116-54068134 chr10:54068118-54068139 chr10:54068121-54068131
5	CTCF	chr10:54068640-54068790	HCPEpiC	choroid plexus:	n/a	n/a
6	CTCF	chr10:54067690-54068968	SK-N-SH	brain:	n/a	chr10:54068119-54068132 chr10:54068119-54068128 chr10:54068116-54068134 chr10:54068118-54068139 chr10:54068121-54068131
7	E2F6	chr10:54068120-54068955	A549	lung:	n/a	chr10:54068852-54068863 chr10:54068640-54068650 chr10:54068855-54068863 chr10:54068856-54068863 chr10:54068854-54068864 chr10:54068847-54068862 chr10:54068855-54068863 chr10:54068853-54068864
8	GTF2F1	chr10:54068078-54068745	H1-hESC	embryonic stem cell:	n/a	n/a
9	HMGN3	chr10:54068588-54068788	K562	blood:	n/a	n/a
10	MAX	chr10:54068438-54068805	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr10:54068210-54068932	A549	lung:	n/a	n/a
12	MAX	chr10:54068016-54068867	HepG2	liver:	n/a	n/a
13	MAX	chr10:54068457-54068855	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr10:54067991-54068974	A549	lung:	n/a	n/a
15	MAZ	chr10:54068001-54068886	HepG2	liver:	n/a	n/a
16	MYBL2	chr10:54068055-54068840	HepG2	liver:	n/a	n/a
17	NFIC	chr10:54068310-54068797	HepG2	liver:	n/a	n/a
18	POLR2A	chr10:54068506-54068752	A549	lung:	n/a	n/a
19	POLR2A	chr10:54067987-54068782	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr10:54068088-54068795	H1-neurons	neurons:	n/a	n/a
21	POLR2A	chr10:54068346-54068792	A549	lung:	n/a	n/a
22	POLR2A	chr10:54068243-54068810	ProgFib	skin:	n/a	n/a
23	POLR2A	chr10:54068439-54068780	Gliobla	brain:	n/a	n/a
24	POLR2A	chr10:54068062-54068789	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr10:54068528-54068757	MCF-7	breast:	n/a	n/a
26	POLR2A	chr10:54068448-54068746	A549	lung:	n/a	n/a
27	RAD21	chr10:54068006-54068823	HepG2	liver:	n/a	chr10:54068117-54068136 chr10:54068711-54068720 chr10:54068122-54068132 chr10:54068120-54068133
28	RAD21	chr10:54067889-54068762	H1-hESC	embryonic stem cell:	n/a	chr10:54068117-54068136 chr10:54068711-54068720 chr10:54068122-54068132 chr10:54068120-54068133
29	RAD21	chr10:54067693-54069018	SK-N-SH	brain:	n/a	chr10:54068117-54068136 chr10:54068711-54068720 chr10:54068122-54068132 chr10:54068120-54068133
30	RAD21	chr10:54067682-54068784	HepG2	liver:	n/a	chr10:54068117-54068136 chr10:54068711-54068720 chr10:54068122-54068132 chr10:54068120-54068133
31	RAD21	chr10:54067854-54068783	H1-hESC	embryonic stem cell:	n/a	chr10:54068117-54068136 chr10:54068711-54068720 chr10:54068122-54068132 chr10:54068120-54068133
32	RCOR1	chr10:54068630-54068739	HepG2	liver:	n/a	n/a
33	SMC3	chr10:54067731-54068986	SK-N-SH	brain:	n/a	chr10:54068121-54068129 chr10:54068122-54068132 chr10:54068118-54068132
34	TAF1	chr10:54068391-54068786	H1-hESC	embryonic stem cell:	n/a	n/a
35	TBP	chr10:54068421-54068758	H1-hESC	embryonic stem cell:	n/a	n/a
36	TCF12	chr10:54067962-54069178	A549	lung:	n/a	n/a
37	TCF7L2	chr10:54068083-54068822	PANC-1	pancreas:	n/a	chr10:54068473-54068489 chr10:54068474-54068488
38	TCF7L2	chr10:54068022-54068773	HCT-116	colon:	n/a	chr10:54068473-54068489 chr10:54068474-54068488
39	YY1	chr10:54068446-54068770	A549	lung:	n/a	chr10:54068633-54068647
40	YY1	chr10:54067936-54068865	HepG2	liver:	n/a	chr10:54068633-54068647
41	ZNF143	chr10:54067953-54068759	H1-hESC	embryonic stem cell:	n/a	chr10:54068150-54068168

No.	Distal block	Cell Line	Cell type
1	chr10:54067639..54070008-chr10:54219109..54220773,2	MCF-7	breast:
2	chr10:54068750..54071230-chr10:54072937..54074524,2	K562	blood:
3	chr10:54065577..54083492-chr10:54193846..54218961,120	MCF-7	breast:
4	chr10:54068768..54071357-chr10:54075695..54080723,4	MCF-7	breast:
5	chr10:54068229..54070730-chr10:54076005..54078630,2	K562	blood:
6	chr10:54068619..54069176-chr10:54326482..54327373,2	MCF-7	breast:
7	chr10:54064374..54069621-chr10:54325572..54329506,5	MCF-7	breast:
8	chr10:54060116..54061619-chr10:54068153..54070919,2	MCF-7	breast:
9	chr10:54068053..54070294-chr10:54245844..54248114,2	MCF-7	breast:
10	chr10:53145130..53146653-chr10:54068648..54071560,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MBL2-5	chr10:54069160-54069297	ENSG00000236671
2	lnc-MBL2-5	chr10:54069160-54069297	NR_038277
3	lnc-MBL2-5	chr10:54069160-54069297	NONHSAT013418

Variant related genes	Relation type
DKK1	TF binding region
ENSG00000231131	chromatin interactions
ENSG00000236671	chromatin interactions
ENSG00000107984	chromatin interactions
MAP2K1	miRNA target sites

Extended variants
information (count: 20 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs556396815	chr10:54068742-54068743	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs531755036	chr10:54068744-54068745	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs114092600	chr10:54068837-54068838	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs183408847	chr10:54068863-54068864	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs187945706	chr10:54068871-54068872	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs1896368	chr10:54068904-54068905	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs368436954	chr10:54068949-54068950	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs371569260	chr10:54068959-54068960	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs191215529	chr10:54068984-54068985	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs77711900	chr10:54069001-54069002	Weak transcription Bivalent Enhancer Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs200222272	chr10:54069062-54069063	Weak transcription Bivalent Enhancer Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
12	rs142220869	chr10:54069065-54069066	Weak transcription Bivalent Enhancer Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
13	rs72167025	chr10:54069066-54069067	Weak transcription Bivalent Enhancer Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
14	rs201765734	chr10:54069076-54069077	Weak transcription Bivalent Enhancer Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
15	rs12777844	chr10:54069078-54069079	Weak transcription Bivalent Enhancer Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
16	rs190135567	chr10:54069079-54069080	Weak transcription Bivalent Enhancer Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
17	rs10646074	chr10:54069080-54069081	Weak transcription Bivalent Enhancer Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
18	rs535177624	chr10:54069132-54069133	Weak transcription Bivalent Enhancer Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
19	rs548576863	chr10:54069172-54069173	Weak transcription Bivalent Enhancer Enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
20	rs192583462	chr10:54069184-54069185	Weak transcription Bivalent Enhancer Enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:64)

Disease	PMID	Source
Pancreatic endocrine tumor	17639061	CNVD
Gastric cancer	17908304	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	CNVD
Melanoma	18172304	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Ewing''s sarcoma	17952124	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	20724749	CNVD
Autism	22495311	CNVD
Esophageal cancer	21851588	CNVD
Prostate cancer	18632612	CNVD
Autism	18414403	CNVD
Cockayne syndrome	18421352	CNVD
Glioblastoma	16823260	CNVD
Medulloblastoma	16968546	CNVD
Neuroblastoma	17533364	CNVD
T-cell lymphomas	19863542	CNVD
Testicular germ cell tumor	18059402	CNVD
Squamous cell cancer	21044232	CNVD
Glioma	21971842	CNVD
Cancer	21637783	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Obesity	21956041	CNVD
Developmental delay	21948486	CNVD
Dysmorphic features	21948486	CNVD
Epilepsy	21948486	CNVD
Intellectual disability	21948486	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21364760	CNVD
small cell lung cancer	20016488	CNVD
Colorectal cancer	16272173	CNVD
Metanephric adenoma	20802469	CNVD
Autism	20841430	CNVD
Mental retardation	17124404	CNVD
Epilepsy	20923578	CNVD
Prostate cancer	16573809	CNVD
Schizophrenia	19329560	CNVD
Heart failure	18772530	CNVD
Heart failure	18854381	CNVD
Hyperglycemia	19060297	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Glioblastoma multiforme	22286061	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Usher syndrome	20538994	CNVD
Glioblastoma multiforme	17002787	CNVD
Cancer	20164919	CNVD

Chromatin state (count:145 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54068000-54068800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr10:54068000-54068800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr10:54068000-54068800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
4	chr10:54068000-54068800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
5	chr10:54068000-54068800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr10:54068000-54068800	Active TSS	Brain Angular Gyrus	brain
7	chr10:54068000-54068800	Bivalent/Poised TSS	Fetal Stomach	stomach
8	chr10:54068000-54068800	Active TSS	Right Ventricle	heart
9	chr10:54068000-54068800	Active TSS	HSMMtube	muscle
10	chr10:54068000-54068800	Active TSS	NH-A	brain
11	chr10:54068000-54069000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr10:54068000-54069000	Active TSS	Brain Anterior Caudate	brain
13	chr10:54068000-54069000	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr10:54068200-54068800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr10:54068200-54068800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
16	chr10:54068200-54068800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr10:54068200-54068800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
18	chr10:54068200-54068800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr10:54068200-54068800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr10:54068200-54068800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
21	chr10:54068200-54068800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr10:54068200-54068800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr10:54068200-54068800	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr10:54068200-54068800	Bivalent/Poised TSS	Primary B cells from cord blood	blood
25	chr10:54068200-54068800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr10:54068200-54068800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr10:54068200-54068800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr10:54068200-54068800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr10:54068200-54068800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr10:54068200-54068800	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr10:54068200-54068800	Active TSS	Aorta	Aorta
32	chr10:54068200-54068800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
33	chr10:54068200-54068800	Active TSS	Brain Hippocampus Middle	brain
34	chr10:54068200-54068800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr10:54068200-54068800	Active TSS	Brain Substantia Nigra	brain
36	chr10:54068200-54068800	Active TSS	Colon Smooth Muscle	Colon
37	chr10:54068200-54068800	Bivalent/Poised TSS	Esophagus	oesophagus
38	chr10:54068200-54068800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
39	chr10:54068200-54068800	Active TSS	Fetal Kidney	kidney
40	chr10:54068200-54068800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
41	chr10:54068200-54068800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
42	chr10:54068200-54068800	Active TSS	Gastric	stomach
43	chr10:54068200-54068800	Enhancers	Lung	lung
44	chr10:54068200-54068800	Flanking Active TSS	Pancreas	Pancrea
45	chr10:54068200-54068800	Active TSS	Placenta Amnion	Placenta Amnion
46	chr10:54068200-54068800	Active TSS	Right Atrium	heart
47	chr10:54068200-54068800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
48	chr10:54068200-54068800	Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr10:54068200-54068800	Active TSS	Stomach Smooth Muscle	stomach
50	chr10:54068200-54068800	Enhancers	Spleen	Spleen

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