Variant report

Variant	esv3321931
Chromosome Location	chr4:3311228-3311994
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:3311769-3311820	GM13976	blood:	n/a	n/a
2	CTCF	chr4:3311163-3311243	Kidney_OC	kidney:	n/a	n/a
3	CTCF	chr4:3311707-3311805	Kidney_OC	kidney:	n/a	n/a
4	CTCF	chr4:3311446-3311511	Kidney_OC	kidney:	n/a	n/a
5	POU2F2	chr4:3310903-3311817	GM12878	blood:	n/a	n/a
6	TAF1	chr4:3310654-3311250	HepG2	liver:	n/a	n/a
7	TCF12	chr4:3311611-3312050	GM12878	blood:	n/a	n/a
8	TCF12	chr4:3311665-3311858	GM12878	blood:	n/a	n/a
9	TCF12	chr4:3311111-3311300	GM12878	blood:	n/a	n/a
10	TCF3	chr4:3310840-3312098	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C4orf44-3	chr4:3311226-3311715	NONHSAT094858
2	lnc-C4orf44-3	chr4:3311824-3312170	NONHSAT094859
3	lnc-C4orf44-3	chr4:3311824-3312124	NONHSAT094858
4	lnc-C4orf44-3	chr4:3311264-3311294	NONHSAT094859

No data

Variant related genes	Relation type
RGS12	TF binding region
ENSG00000248840	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:78 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs74184934	chr4:3311233-3311234	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
2	rs111677495	chr4:3311237-3311238	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
3	rs563735885	chr4:3311268-3311269	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
4	rs201640815	chr4:3311286-3311287	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
5	rs71636717	chr4:3311300-3311301	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
6	rs113254070	chr4:3311312-3311313	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
7	rs111620481	chr4:3311313-3311314	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
8	rs113677374	chr4:3311336-3311337	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
9	rs61790545	chr4:3311354-3311355	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	mRNA abundance
10	rs73795503	chr4:3311370-3311371	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
11	rs73795505	chr4:3311371-3311372	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
12	rs113543952	chr4:3311390-3311391	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
13	rs147612830	chr4:3311406-3311407	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	mRNA abundance
14	rs200077956	chr4:3311420-3311421	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
15	rs78517204	chr4:3311421-3311422	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
16	rs112496574	chr4:3311424-3311425	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
17	rs574201593	chr4:3311441-3311442	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
18	rs111904104	chr4:3311498-3311499	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
19	rs374927477	chr4:3311512-3311513	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
20	rs367549778	chr4:3311524-3311525	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
21	rs371826452	chr4:3311525-3311526	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
22	rs142176308	chr4:3311533-3311534	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
23	rs10023046	chr4:3311548-3311549	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
24	rs370971282	chr4:3311569-3311570	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
25	rs59586116	chr4:3311571-3311572	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
26	rs61790546	chr4:3311575-3311576	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
27	rs561857244	chr4:3311583-3311584	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
28	rs6831778	chr4:3311596-3311597	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
29	rs6845637	chr4:3311599-3311600	Weak transcription Enhancers	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
30	rs527532899	chr4:3311616-3311617	Weak transcription Enhancers Active TSS	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
31	rs55905213	chr4:3311632-3311633	Weak transcription Enhancers Active TSS	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
32	rs56359978	chr4:3311633-3311634	Weak transcription Enhancers Active TSS	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
33	rs71589616	chr4:3311638-3311639	Weak transcription Enhancers Active TSS	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
34	rs10023136	chr4:3311652-3311653	Weak transcription Enhancers Active TSS	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
35	rs56749438	chr4:3311656-3311657	Weak transcription Enhancers Active TSS	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
36	rs58672522	chr4:3311669-3311670	Weak transcription Enhancers Active TSS	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
37	rs34746766	chr4:3311671-3311672	Weak transcription Enhancers Active TSS	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
38	rs61367409	chr4:3311685-3311686	Weak transcription Enhancers Active TSS	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
39	rs59939497	chr4:3311686-3311687	Weak transcription Enhancers Active TSS	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
40	rs112083618	chr4:3311704-3311705	Weak transcription Enhancers Active TSS	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
41	rs61790547	chr4:3311705-3311706	Weak transcription Enhancers Active TSS	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
42	rs61462434	chr4:3311709-3311710	Weak transcription Enhancers Active TSS	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
43	rs199972653	chr4:3311712-3311713	Weak transcription Enhancers Active TSS	TF binding region lncRNA	2 gene(s)	Overlapped CNVs	n/a
44	rs55654819	chr4:3311722-3311723	Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
45	rs80112739	chr4:3311738-3311739	Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
46	rs71589615	chr4:3311742-3311743	Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
47	rs56684004	chr4:3311754-3311755	Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
48	rs71608273	chr4:3311756-3311757	Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
49	rs58205019	chr4:3311757-3311758	Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
50	rs66518310	chr4:3311761-3311762	Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:55)

Disease	PMID	Source
Retinitis pigmentosa	18421352	CNVD
Wolf-Hirschhorn syndrome	19259404	CNVD
Bladder cancer	19242612	CNVD
Breast cancer	19242612	CNVD
Congenital anomalies of the kidney and urinary tract	19242612	CNVD
abnormal development	18461090	CNVD
Olfactory neuroblastoma	18408657	CNVD
Wilms tumour	21544195	CNVD
Melanoma	20688739	CNVD
Colorectal cancer	16272173	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
small cell lung cancer	20016488	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	21399695	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3296600-3318600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:3299600-3318600	Weak transcription	Aorta	Aorta
3	chr4:3301200-3350000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:3301600-3312400	Enhancers	Fetal Muscle Trunk	muscle
5	chr4:3304000-3313000	Weak transcription	HepG2	liver
6	chr4:3304800-3318600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:3306600-3312600	Enhancers	Lung	lung
8	chr4:3306600-3320600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:3306800-3312400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr4:3306800-3312800	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr4:3307000-3320600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr4:3307200-3318000	Weak transcription	Liver	Liver
13	chr4:3307200-3327000	Weak transcription	Fetal Kidney	kidney
14	chr4:3307400-3312200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr4:3307400-3325600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:3307400-3326800	Weak transcription	A549	lung
17	chr4:3307600-3315000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:3307600-3322200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:3307600-3323000	Weak transcription	NH-A	brain
20	chr4:3307600-3323600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:3307800-3311600	Weak transcription	Fetal Intestine Large	intestine
22	chr4:3307800-3312200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr4:3307800-3319000	Weak transcription	Colon Smooth Muscle	Colon
24	chr4:3308000-3311600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr4:3308000-3313400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:3308000-3318200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:3308000-3318600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr4:3308000-3319800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr4:3308000-3322800	Weak transcription	NHDF-Ad	bronchial
30	chr4:3308000-3323600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr4:3308000-3323800	Weak transcription	Osteobl	bone
32	chr4:3308000-3326000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:3308000-3327000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr4:3308200-3311800	Weak transcription	Psoas Muscle	Psoas
35	chr4:3308200-3314400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:3308200-3318400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr4:3308200-3318400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr4:3308200-3318600	Weak transcription	NHLF	lung
39	chr4:3308200-3319800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr4:3308200-3320400	Weak transcription	Fetal Heart	heart
41	chr4:3308200-3323200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr4:3308400-3314200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:3308400-3315000	Weak transcription	Primary T cells from cord blood	blood
44	chr4:3308400-3317800	Weak transcription	HSMM	muscle
45	chr4:3308400-3318200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr4:3308400-3318200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr4:3308400-3320200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr4:3308400-3321400	Weak transcription	Stomach Mucosa	stomach
49	chr4:3308600-3312400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:3308600-3317400	Weak transcription	Pancreas	Pancrea

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