Variant report

Variant	esv3325048
Chromosome Location	chr4:3227704-3230502
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	CTCF	chr4:3230120-3230270	GM12865	blood:	n/a	n/a
2	EP300	chr4:3227883-3227934	GM12878	blood:	n/a	n/a
3	MXI1	chr4:3229855-3230358	IMR90	lung:	n/a	n/a
4	POLR2A	chr4:3229767-3229966	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:3228813-3228958	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr4:3228750-3229117	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:3230095-3230447	GM12891	blood:	n/a	n/a
8	POLR2A	chr4:3228031-3228277	HepG2	liver:	n/a	n/a
9	POLR2A	chr4:3227972-3228074	GM12878	blood:	n/a	n/a
10	POLR2A	chr4:3227821-3227913	HepG2	liver:	n/a	n/a
11	POLR2A	chr4:3229618-3230488	GM12892	blood:	n/a	n/a
12	POLR2A	chr4:3229907-3230299	GM12878	blood:	n/a	n/a
13	POLR2A	chr4:3227792-3227954	GM12878	blood:	n/a	n/a
14	POLR2A	chr4:3230203-3230458	GM12878	blood:	n/a	n/a
15	POLR2A	chr4:3229868-3230008	HepG2	liver:	n/a	n/a
16	POLR2A	chr4:3229639-3229983	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3225798..3228316-chr4:3230639..3233767,3	K562	blood:
2	chr4:3225798..3227751-chr4:3230639..3233084,3	K562	blood:

Variant related genes	Relation type
HTT	TF binding region

Extended variants
information (count: 112 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:112 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs367759097	chr4:3227734-3227735	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
2	rs73074831	chr4:3227753-3227754	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs140762692	chr4:3227806-3227807	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs3129324	chr4:3227824-3227825	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs4690078	chr4:3227860-3227861	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs562018902	chr4:3227882-3227883	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs564330431	chr4:3227908-3227909	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs149793197	chr4:3227915-3227916	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs547346556	chr4:3227956-3227957	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs570747858	chr4:3228011-3228012	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs539869936	chr4:3228040-3228041	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs549983282	chr4:3228074-3228075	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs191292163	chr4:3228153-3228154	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs148972854	chr4:3228174-3228175	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs143777528	chr4:3228221-3228222	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs554823259	chr4:3228227-3228228	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs551553857	chr4:3228243-3228244	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs377567916	chr4:3228249-3228250	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs534087864	chr4:3228286-3228287	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs114705279	chr4:3228300-3228301	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs560345383	chr4:3228323-3228324	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs545820534	chr4:3228330-3228331	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs562412203	chr4:3228338-3228339	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs576112872	chr4:3228339-3228340	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs527754846	chr4:3228346-3228347	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs549085397	chr4:3228347-3228348	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs541973459	chr4:3228467-3228468	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs2237006	chr4:3228492-3228493	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs537860972	chr4:3228526-3228527	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs114194615	chr4:3228547-3228548	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs374107224	chr4:3228644-3228645	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs74653830	chr4:3228658-3228659	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs564828637	chr4:3228676-3228677	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs533157014	chr4:3228728-3228729	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs183613186	chr4:3228816-3228817	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs146623302	chr4:3228818-3228819	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs141414849	chr4:3228822-3228823	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs373684946	chr4:3228827-3228828	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs189486178	chr4:3228877-3228878	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs192437466	chr4:3228882-3228883	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs569054944	chr4:3228890-3228891	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs185403682	chr4:3228891-3228892	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs553769008	chr4:3228895-3228896	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs145187067	chr4:3228914-3228915	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs190082652	chr4:3228934-3228935	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs3135055	chr4:3228966-3228967	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs111524241	chr4:3228981-3228982	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs556130421	chr4:3228993-3228994	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs375605275	chr4:3229000-3229001	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs202201793	chr4:3229049-3229050	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 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 cancer	17952125	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:258 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
2	chr4:3145800-3239200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:3172400-3238800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr4:3193800-3233000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:3194000-3237600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:3196000-3242600	Strong transcription	Fetal Intestine Small	intestine
7	chr4:3201400-3238400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:3204800-3246000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:3205800-3228000	Strong transcription	Left Ventricle	heart
10	chr4:3206000-3234800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:3206000-3244600	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr4:3206000-3246400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:3206400-3229600	Strong transcription	Fetal Stomach	stomach
14	chr4:3207200-3229000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:3207600-3238600	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:3207600-3243600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr4:3207600-3244000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:3207600-3244600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr4:3207600-3245400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:3207600-3246400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr4:3207800-3228200	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr4:3207800-3228400	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr4:3207800-3229000	Strong transcription	Aorta	Aorta
24	chr4:3207800-3229800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:3207800-3243200	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:3207800-3243800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr4:3207800-3244400	Strong transcription	Duodenum Mucosa	Duodenum
28	chr4:3207800-3245400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:3208000-3235800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:3208000-3243600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr4:3208200-3228400	Strong transcription	Stomach Smooth Muscle	stomach
32	chr4:3208200-3237400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr4:3208200-3239200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:3208200-3246400	Strong transcription	Fetal Thymus	thymus
35	chr4:3208400-3228000	Strong transcription	Brain Cingulate Gyrus	brain
36	chr4:3208400-3228000	Strong transcription	Colonic Mucosa	Colon
37	chr4:3208400-3244800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:3209800-3229400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:3210000-3228000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:3210000-3230200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr4:3210000-3244200	Strong transcription	Fetal Intestine Large	intestine
42	chr4:3210000-3245000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:3210000-3246600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr4:3210200-3230800	Strong transcription	Spleen	Spleen
45	chr4:3210200-3232400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr4:3210400-3247000	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr4:3210600-3229000	Strong transcription	Brain Germinal Matrix	brain
48	chr4:3211000-3230800	Strong transcription	Gastric	stomach
49	chr4:3211600-3246400	Strong transcription	Thymus	Thymus
50	chr4:3213400-3227800	Strong transcription	Duodenum Smooth Muscle	Duodenum

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