Variant report

Variant	esv3404482
Chromosome Location	chr3:112726791-112727222
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112726403..112732813-chr3:112735056..112739637,9	MCF-7	breast:
2	chr3:112723308..112727086-chr3:112729971..112732710,4	MCF-7	breast:
3	chr3:112724378..112727049-chr3:112733822..112736411,3	K562	blood:
4	chr3:112709111..112712767-chr3:112725826..112728376,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD200R1-1	chr3:112727018-112727647	NONHSAT091203

Variant related genes	Relation type
ENSG00000163607	chromatin interactions
ENSG00000240057	chromatin interactions
ENSG00000272844	chromatin interactions
ENSG00000163608	chromatin interactions

Extended variants
information (count: 31 )
Associated
traits (count: 58 )

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	rs531259326	chr3:112726800-112726801	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs559239577	chr3:112726806-112726807	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs577454800	chr3:112726861-112726862	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs544920091	chr3:112726898-112726899	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs367985697	chr3:112726902-112726903	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs115478816	chr3:112726903-112726904	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
7	rs575210396	chr3:112726911-112726912	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
8	rs542275166	chr3:112726913-112726914	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
9	rs560654608	chr3:112726915-112726916	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
10	rs528219334	chr3:112726917-112726918	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
11	rs540027452	chr3:112726918-112726919	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
12	rs148171352	chr3:112726962-112726963	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
13	rs185615829	chr3:112726965-112726966	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
14	rs201750296	chr3:112726968-112726969	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
15	rs377077729	chr3:112726991-112726992	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
16	rs199942791	chr3:112726992-112726993	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
17	rs189931000	chr3:112726994-112726995	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
18	rs111968076	chr3:112726999-112727000	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
19	rs146190936	chr3:112727040-112727041	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
20	rs137888723	chr3:112727048-112727049	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
21	rs149448097	chr3:112727049-112727050	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
22	rs562705546	chr3:112727066-112727067	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
23	rs199628917	chr3:112727078-112727079	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
24	rs143962989	chr3:112727085-112727086	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
25	rs528926961	chr3:112727118-112727119	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
26	rs148625108	chr3:112727168-112727169	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
27	rs374956519	chr3:112727169-112727170	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
28	rs2306857	chr3:112727184-112727185	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
29	rs2306858	chr3:112727199-112727200	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs369058611	chr3:112727207-112727208	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
31	rs62265060	chr3:112727222-112727223	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:58)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Neurodevelopmental disorder	22521361	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	16608533	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Developmental delay	22180640	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Multiple myeloma	17550852	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Basal cell lymphoma	21115979	CNVD
Attention deficit hyperactivity disorder	22180640	CNVD
Breast cancer	17142309	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:156 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112710400-112737400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:112711400-112736600	Weak transcription	Stomach Mucosa	stomach
3	chr3:112712200-112736800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:112712400-112736600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:112712800-112736600	Weak transcription	Fetal Heart	heart
6	chr3:112714400-112736800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:112715000-112735800	Strong transcription	Primary B cells from cord blood	blood
8	chr3:112715200-112736000	Strong transcription	Primary hematopoietic stem cells	blood
9	chr3:112715600-112734600	Strong transcription	Liver	Liver
10	chr3:112715600-112736600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:112715600-112736600	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:112715800-112735800	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr3:112715800-112736000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:112715800-112736200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:112715800-112736800	Strong transcription	Placenta	Placenta
16	chr3:112716000-112736000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr3:112716000-112736600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr3:112716200-112735800	Strong transcription	A549	lung
19	chr3:112716400-112735600	Strong transcription	Adipose Nuclei	Adipose
20	chr3:112716400-112736400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:112716400-112736400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:112716800-112726800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:112716800-112727000	Strong transcription	Fetal Brain Female	brain
24	chr3:112716800-112729200	Strong transcription	Fetal Lung	lung
25	chr3:112716800-112734400	Strong transcription	GM12878-XiMat	blood
26	chr3:112716800-112735800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:112716800-112736200	Strong transcription	Duodenum Mucosa	Duodenum
28	chr3:112716800-112736400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:112716800-112736400	Strong transcription	NH-A	brain
30	chr3:112716800-112736600	Strong transcription	Osteobl	bone
31	chr3:112716800-112736800	Strong transcription	HSMM	muscle
32	chr3:112717000-112729600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:112717000-112729600	Strong transcription	Fetal Intestine Large	intestine
34	chr3:112717000-112736400	Strong transcription	Primary B cells from peripheral blood	blood
35	chr3:112717200-112728000	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:112717200-112736000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:112717200-112736200	Strong transcription	HMEC	breast
38	chr3:112717400-112733200	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr3:112718400-112736200	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr3:112718600-112728000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:112718600-112729400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:112718600-112735800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:112719600-112728000	Strong transcription	Hela-S3	cervix
44	chr3:112719800-112729600	Strong transcription	Brain Anterior Caudate	brain
45	chr3:112720000-112727800	Strong transcription	HUVEC	blood vessel
46	chr3:112720000-112736400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:112720400-112730000	Strong transcription	Fetal Kidney	kidney
48	chr3:112720800-112729800	Strong transcription	Fetal Muscle Leg	muscle
49	chr3:112721000-112727400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr3:112721000-112729600	Strong transcription	Sigmoid Colon	Sigmoid Colon

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