Variant report

Variant	esv2762594
Chromosome Location	chr6:54159146-54168766
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	CEBPB	chr6:54164359-54164641	IMR90	lung:	n/a	n/a
2	CEBPB	chr6:54168276-54168476	H1-hESC	embryonic stem cell:	n/a	chr6:54168414-54168427
3	CEBPB	chr6:54166134-54166210	H1-hESC	embryonic stem cell:	n/a	n/a
4	CEBPB	chr6:54168233-54168605	Hela-S3	cervix:	n/a	chr6:54168414-54168427
5	CEBPB	chr6:54168309-54168547	IMR90	lung:	n/a	chr6:54168414-54168427
6	CTCF	chr6:54159257-54159317	GM20000	blood:	n/a	n/a
7	CTCF	chr6:54160254-54160344	MCF-7	breast:	n/a	n/a
8	CTCF	chr6:54160258-54160327	GM19239	blood:	n/a	n/a
9	CTCF	chr6:54160292-54160328	MCF-7	breast:	n/a	n/a
10	CTCF	chr6:54160328-54160335	GM19239	blood:	n/a	n/a
11	CTCF	chr6:54160334-54160344	MCF-7	breast:	n/a	n/a
12	EP300	chr6:54164380-54165016	SK-N-SH_RA	brain:	n/a	chr6:54164826-54164835
13	EP300	chr6:54164349-54165010	SK-N-SH_RA	brain:	n/a	chr6:54164826-54164835
14	EP300	chr6:54164014-54165542	SK-N-SH	brain:	n/a	chr6:54164826-54164835
15	EP300	chr6:54164218-54165234	SK-N-SH	brain:	n/a	chr6:54164826-54164835
16	FOS	chr6:54164752-54164906	MCF10A-Er-Src	breast:	n/a	chr6:54164825-54164835 chr6:54164826-54164834 chr6:54164826-54164833 chr6:54164826-54164834 chr6:54164824-54164836
17	FOS	chr6:54164754-54164944	MCF10A-Er-Src	breast:	n/a	chr6:54164825-54164835 chr6:54164826-54164834 chr6:54164826-54164833 chr6:54164826-54164834 chr6:54164824-54164836
18	FOS	chr6:54168398-54168451	MCF10A-Er-Src	breast:	n/a	n/a
19	FOS	chr6:54158887-54159189	HUVEC	blood vessel:	n/a	chr6:54159038-54159049
20	FOS	chr6:54168408-54168445	MCF10A-Er-Src	breast:	n/a	n/a
21	FOSL2	chr6:54164213-54165132	SK-N-SH	brain:	n/a	chr6:54164825-54164835 chr6:54164826-54164834 chr6:54164826-54164833 chr6:54164826-54164834 chr6:54164824-54164836
22	GATA3	chr6:54164080-54165265	SK-N-SH	brain:	n/a	chr6:54164923-54164940 chr6:54164824-54164833
23	GATA3	chr6:54164203-54165212	SK-N-SH	brain:	n/a	chr6:54164923-54164940 chr6:54164824-54164833
24	JUND	chr6:54164176-54165168	SK-N-SH	brain:	n/a	chr6:54164825-54164835 chr6:54164826-54164834 chr6:54164826-54164833 chr6:54164826-54164834 chr6:54164824-54164836
25	JUND	chr6:54164020-54165163	SK-N-SH	brain:	n/a	chr6:54164825-54164835 chr6:54164826-54164834 chr6:54164108-54164119 chr6:54164826-54164833 chr6:54164826-54164834 chr6:54164824-54164836
26	JUND	chr6:54164199-54165089	SK-N-SH	brain:	n/a	chr6:54164825-54164835 chr6:54164826-54164834 chr6:54164826-54164833 chr6:54164826-54164834 chr6:54164824-54164836
27	MAX	chr6:54164924-54165017	NB4	blood:	n/a	n/a
28	MYC	chr6:54160240-54160242	MCF-7	breast:	n/a	n/a
29	MYC	chr6:54160287-54160297	MCF-7	breast:	n/a	n/a
30	MYC	chr6:54160099-54160223	H1-hESC	embryonic stem cell:	n/a	n/a
31	MYC	chr6:54160259-54160285	MCF-7	breast:	n/a	n/a
32	MYC	chr6:54160186-54160208	MCF-7	breast:	n/a	n/a
33	NFIC	chr6:54164314-54165074	SK-N-SH	brain:	n/a	n/a
34	PBX3	chr6:54164214-54165159	SK-N-SH	brain:	n/a	n/a
35	PBX3	chr6:54163971-54165205	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr6:54164150-54164292	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr6:54159864-54160509	MCF-7	breast:	n/a	n/a
38	POLR2A	chr6:54159852-54160327	MCF-7	breast:	n/a	n/a
39	POLR2A	chr6:54164315-54164980	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr6:54164334-54164528	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr6:54164595-54164603	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr6:54160380-54160383	Gliobla	brain:	n/a	n/a
43	POLR2A	chr6:54160214-54160373	Gliobla	brain:	n/a	n/a
44	POLR2A	chr6:54161259-54161332	MCF10A-Er-Src	breast:	n/a	n/a
45	STAT3	chr6:54164810-54164987	MCF10A-Er-Src	breast:	n/a	n/a
46	TCF12	chr6:54164128-54165213	SK-N-SH	brain:	n/a	n/a
47	TCF12	chr6:54164048-54165263	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:54164489..54166885-chr6:54172521..54174692,2	MCF-7	breast:

Variant related genes	Relation type
TINAG	TF binding region
ENSG00000137251	chromatin interactions

Extended variants
information (count: 430 )
Associated
traits (count: 79 )

Variant overlapped rSNPs/rCNVs (count:430 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12215705	chr6:54159146-54159147	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs548208826	chr6:54159163-54159164	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs568395622	chr6:54159237-54159238	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs34906236	chr6:54159267-54159268	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs377716549	chr6:54159278-54159279	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs534185282	chr6:54159284-54159285	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs142055709	chr6:54159290-54159291	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs558573697	chr6:54159383-54159384	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs182426613	chr6:54159386-54159387	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs146293642	chr6:54159403-54159404	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs555975989	chr6:54159406-54159407	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs1605674	chr6:54159427-54159428	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs540938369	chr6:54159434-54159435	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs74819233	chr6:54159480-54159481	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs555367596	chr6:54159481-54159482	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs111617670	chr6:54159514-54159515	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs572094419	chr6:54159539-54159540	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs187091264	chr6:54159558-54159559	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs564416386	chr6:54159591-54159592	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs9395929	chr6:54159663-54159664	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs114294748	chr6:54159727-54159728	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs562816544	chr6:54159740-54159741	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs531722545	chr6:54159777-54159778	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs139268455	chr6:54159779-54159780	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs546716001	chr6:54159785-54159786	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs184946924	chr6:54159787-54159788	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs150057666	chr6:54159802-54159803	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs547645522	chr6:54159808-54159809	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
29	rs571165029	chr6:54159832-54159833	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs145429387	chr6:54159838-54159839	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs114598489	chr6:54159855-54159856	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
32	rs7775058	chr6:54159866-54159867	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
33	rs148769853	chr6:54159868-54159869	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
34	rs7774931	chr6:54159874-54159875	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs189830962	chr6:54159887-54159888	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
36	rs376362901	chr6:54159891-54159892	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
37	rs138128519	chr6:54159892-54159893	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
38	rs371424686	chr6:54159901-54159902	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
39	rs557762565	chr6:54159912-54159913	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
40	rs578250628	chr6:54159913-54159914	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
41	rs9370281	chr6:54159914-54159915	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs7740868	chr6:54159915-54159916	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
43	rs537708827	chr6:54159940-54159941	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs77624752	chr6:54159949-54159950	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs111880683	chr6:54159962-54159963	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs116781420	chr6:54159967-54159968	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs568452832	chr6:54159976-54159977	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs561858518	chr6:54159982-54159983	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs78221110	chr6:54160003-54160004	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
50	rs9370282	chr6:54160004-54160005	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:79)

Disease	PMID	Source
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Leukemia	21518781	CNVD
Cancer	21637783	CNVD
Facial dysmorphism	22105932	CNVD
Medulloblastoma	21979893	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Endometrial cancer	22040021	CNVD
Acute myeloid leukemia	16864856	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Bladder cancer	19088036	CNVD
Wilms tumour	21544195	CNVD
Uveal melanoma	21693616	CNVD
Biliary cancer	19435499	CNVD
Malaria	21533027	CNVD
Retinoblastoma	19183342	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21858162	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	21448237	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	22495311	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Urothelial carcinoma	18382360	CNVD
Cancer	21183584	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
Gastric cancer	17908304	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Neuroblastoma	16790693	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Osteosarcoma	16790693	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Lung cancer	18438408	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	17603634	CNVD
Neurocytoma	17123091	CNVD
Systemic lupus erythematosus	17503323	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Breast cancer	16608533	CNVD
Melanoma	18172304	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Neuroblastoma	19686582	CNVD
Neuroblastoma	17289879	CNVD
Breast cancer	17899364	CNVD
Breast cancer	17133270	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Colorectal cancer	16912164	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
Breast cancer	22522925	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54153800-54160000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:54156200-54159800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:54157200-54164000	Weak transcription	NHDF-Ad	bronchial
4	chr6:54157600-54162200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:54157600-54164000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:54158600-54159400	Enhancers	HUVEC	blood vessel
7	chr6:54158800-54159800	Enhancers	NH-A	brain
8	chr6:54159400-54160400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:54159600-54159800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:54159800-54160400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:54159800-54160800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:54160000-54160200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:54160400-54161000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:54160800-54161000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:54164000-54164200	Enhancers	NHDF-Ad	bronchial
16	chr6:54164000-54164600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr6:54164000-54164800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:54164200-54164400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:54164200-54164600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:54164200-54164600	Flanking Active TSS	NHDF-Ad	bronchial
21	chr6:54164400-54164600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:54164600-54165400	Enhancers	NHLF	lung
23	chr6:54164600-54166200	Enhancers	NHDF-Ad	bronchial
24	chr6:54164800-54166800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:54165200-54165400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:54166600-54167200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:54167600-54168800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:54168400-54168800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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