Variant report

Variant	esv3525773
Chromosome Location	chr2:86268386-86268627
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	chr2:86268153-86268416	IMR90	lung:	n/a	n/a
2	CTCF	chr2:86268207-86268429	GM19239	blood:	n/a	n/a
3	CTCF	chr2:86268150-86268448	K562	blood:	n/a	n/a
4	CTCF	chr2:86268240-86268390	BJ	skin:	n/a	n/a
5	CTCF	chr2:86268091-86268405	GM12878	blood:	n/a	n/a
6	CTCF	chr2:86268214-86268533	GM12891	blood:	n/a	n/a
7	CTCF	chr2:86268140-86268410	HVMF	connective:	n/a	n/a
8	CTCF	chr2:86268151-86268413	K562	blood:	n/a	n/a
9	CTCF	chr2:86268025-86268515	MCF-7	breast:	n/a	n/a
10	CTCF	chr2:86268320-86268470	HFF-Myc	foreskin:	n/a	n/a
11	CTCF	chr2:86268160-86268430	HFF-Myc	foreskin:	n/a	n/a
12	CTCF	chr2:86268218-86268393	GM19238	blood:	n/a	n/a
13	CTCF	chr2:86268260-86268410	HCM	heart:	n/a	n/a
14	CTCF	chr2:86268225-86268410	GM12892	blood:	n/a	n/a
15	CTCF	chr2:86268189-86268392	MCF-7	breast:	n/a	n/a
16	CTCF	chr2:86268156-86268404	K562	blood:	n/a	n/a
17	FOXA1	chr2:86268229-86268406	T-47D	breast:	n/a	n/a
18	FOXA2	chr2:86268167-86268465	HepG2	liver:	n/a	n/a
19	GABPA	chr2:86268196-86268586	K562	blood:	n/a	chr2:86268487-86268501 chr2:86268484-86268498
20	GABPA	chr2:86268033-86268595	MCF-7	breast:	n/a	chr2:86268487-86268501 chr2:86268484-86268498
21	GABPA	chr2:86268191-86268568	HepG2	liver:	n/a	chr2:86268487-86268501 chr2:86268484-86268498
22	GABPA	chr2:86268127-86268489	A549	lung:	n/a	n/a
23	GATA3	chr2:86268129-86268583	MCF-7	breast:	n/a	n/a
24	MYC	chr2:86268241-86268457	MCF-7	breast:	n/a	n/a
25	POLR2A	chr2:86268614-86268778	K562	blood:	n/a	n/a
26	POLR2A	chr2:86268225-86268599	GM12878	blood:	n/a	n/a
27	POLR2A	chr2:86268493-86269034	K562	blood:	n/a	n/a
28	POLR2A	chr2:86267736-86268834	HepG2	liver:	n/a	n/a
29	POLR2A	chr2:86268176-86268859	K562	blood:	n/a	n/a
30	POLR2A	chr2:86268350-86268390	ProgFib	skin:	n/a	n/a
31	POLR2A	chr2:86268453-86268461	MCF-7	breast:	n/a	n/a
32	POLR2A	chr2:86268152-86268546	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr2:86268141-86268845	GM12892	blood:	n/a	n/a
34	POLR2A	chr2:86268286-86268391	K562	blood:	n/a	n/a
35	POLR2A	chr2:86268283-86268447	MCF-7	breast:	n/a	n/a
36	POLR2A	chr2:86268213-86268430	GM12878	blood:	n/a	n/a
37	RUNX3	chr2:86268059-86268472	GM12878	blood:	n/a	n/a
38	SMC3	chr2:86268214-86268392	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86263075..86266284-chr2:86266783..86270779,4	MCF-7	breast:

Variant related genes	Relation type
POLR1A	TF binding region
ENSG00000068654	chromatin interactions

Extended variants
information (count: 19 )
Associated
traits (count: 50 )

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs60183243	chr2:86268387-86268388	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs547770423	chr2:86268406-86268407	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs575014795	chr2:86268407-86268408	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs540684068	chr2:86268444-86268445	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs535653424	chr2:86268457-86268458	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs145985805	chr2:86268473-86268474	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs576394201	chr2:86268474-86268475	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs554499181	chr2:86268485-86268486	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs572641403	chr2:86268487-86268488	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs116470570	chr2:86268489-86268490	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs555324409	chr2:86268490-86268491	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs9677675	chr2:86268494-86268495	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs576000349	chr2:86268498-86268499	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs543496319	chr2:86268513-86268514	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs141600019	chr2:86268514-86268515	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs543544469	chr2:86268521-86268522	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs562020038	chr2:86268556-86268557	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs529944937	chr2:86268588-86268589	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs143862612	chr2:86268611-86268612	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:50)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Medulloblastoma	21979893	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Medulloblastoma	20607354	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Neurodevelopmental disorder	22521361	CNVD
Lung cancer	18438408	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Seminomas	18059402	CNVD
Testicular germ cell tumor	18059402	CNVD
Myxofibrosarcoma	16751306	CNVD
small cell lung cancer	20016488	CNVD
Acute myeloid leukemia	21251322	CNVD
Breast cancer	16272173	CNVD
Breast cancer	20409316	CNVD
Breast cancer	21990379	CNVD
Astrocytoma	22246337	CNVD
Papillary thyroid carcinoma	22161024	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	21399695	CNVD
Breast cancer	21364760	CNVD
Schizophrenia	21346763	CNVD
Autism	22495309	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:136 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86251200-86273200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr2:86251200-86281400	Strong transcription	H9 Cell Line	embryonic stem cell
3	chr2:86251200-86283000	Strong transcription	HepG2	liver
4	chr2:86251200-86283200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:86251200-86285000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:86251200-86285200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:86252200-86282600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:86252200-86285200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:86252400-86283200	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr2:86252600-86276800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:86260600-86268800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:86260600-86269000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr2:86260800-86268800	Weak transcription	Ovary	ovary
15	chr2:86261200-86272000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:86262400-86268400	Flanking Active TSS	Thymus	Thymus
17	chr2:86263800-86268800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:86263800-86269200	Enhancers	Primary T cells fromperipheralblood	blood
19	chr2:86264000-86269000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:86264000-86281800	Strong transcription	Fetal Brain Female	brain
21	chr2:86264000-86332000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr2:86264200-86268400	Enhancers	Primary T cells from cord blood	blood
23	chr2:86264200-86269600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:86264200-86275400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:86264400-86269000	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr2:86264400-86269800	Genic enhancers	Fetal Muscle Trunk	muscle
27	chr2:86264400-86279400	Strong transcription	Hela-S3	cervix
28	chr2:86264400-86285400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:86264400-86285400	Strong transcription	A549	lung
30	chr2:86264600-86273800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:86264800-86269800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr2:86264800-86273000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:86264800-86275400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
34	chr2:86265000-86269800	Genic enhancers	Fetal Muscle Leg	muscle
35	chr2:86265200-86268800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr2:86265200-86268800	Genic enhancers	Dnd41	blood
37	chr2:86265200-86281600	Strong transcription	HMEC	breast
38	chr2:86265200-86284000	Strong transcription	NHEK	skin
39	chr2:86265200-86330000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:86265400-86269000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:86265400-86269200	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr2:86265400-86282600	Strong transcription	Esophagus	oesophagus
43	chr2:86265400-86285200	Strong transcription	Fetal Intestine Large	intestine
44	chr2:86265400-86289800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:86265400-86289800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:86265600-86270200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
47	chr2:86265600-86270200	Strong transcription	NH-A	brain
48	chr2:86265600-86272600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr2:86265600-86273200	Strong transcription	Aorta	Aorta
50	chr2:86265600-86274600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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