Variant report

Variant	esv3336526
Chromosome Location	chr6:37475076-37476236
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	CHD2	chr6:37474976-37475081	H1-hESC	embryonic stem cell:	n/a	n/a
2	GATA2	chr6:37475796-37476436	SH-SY5Y	brain:	n/a	n/a
3	GATA3	chr6:37475752-37476099	T-47D	breast:	n/a	n/a
4	GATA3	chr6:37475960-37476160	SH-SY5Y	brain:	n/a	n/a
5	GATA3	chr6:37475715-37476126	T-47D	breast:	n/a	n/a
6	NFYB	chr6:37474916-37475188	Hela-S3	cervix:	n/a	chr6:37475063-37475078
7	NFYB	chr6:37474878-37475097	K562	blood:	n/a	chr6:37475063-37475078
8	NFYB	chr6:37474873-37475155	GM12878	blood:	n/a	chr6:37475063-37475078
9	SP1	chr6:37474931-37475176	H1-hESC	embryonic stem cell:	n/a	n/a
10	TCF12	chr6:37475727-37475962	GM12878	blood:	n/a	n/a
11	TCF3	chr6:37475736-37475902	GM12878	blood:	n/a	chr6:37475769-37475779
12	TCF3	chr6:37475683-37476034	GM12878	blood:	n/a	chr6:37475769-37475779
13	USF1	chr6:37474907-37475263	H1-hESC	embryonic stem cell:	n/a	n/a
14	USF1	chr6:37474935-37475195	H1-hESC	embryonic stem cell:	n/a	n/a
15	USF2	chr6:37474905-37475229	H1-hESC	embryonic stem cell:	n/a	n/a
16	ZNF143	chr6:37475940-37475968	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:37454885..37456493-chr6:37473067..37475104,2	K562	blood:
2	chr6:37463837..37466464-chr6:37476098..37478071,3	K562	blood:
3	chr6:37475829..37477406-chr6:37481172..37483865,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FTSJD2-1	chr6:37475124-37475480	ENSG00000204110.5
2	lnc-FTSJD2-1	chr6:37475124-37475480	ENSG00000204110.5

Variant related genes	Relation type
ENSG00000204110	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 91 )

Variant overlapped rSNPs/rCNVs (count:65 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs540642941	chr6:37475080-37475081	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs35054929	chr6:37475085-37475086	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs34392394	chr6:37475092-37475093	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs35856320	chr6:37475106-37475107	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs143656363	chr6:37475135-37475136	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs529591232	chr6:37475157-37475158	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs138287026	chr6:37475159-37475160	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs9462316	chr6:37475189-37475190	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs116304941	chr6:37475203-37475204	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
10	rs78047532	chr6:37475238-37475239	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
11	rs80282935	chr6:37475243-37475244	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
12	rs35231469	chr6:37475244-37475245	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs546452814	chr6:37475263-37475264	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
14	rs13194564	chr6:37475274-37475275	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs532007489	chr6:37475352-37475353	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs184041948	chr6:37475353-37475354	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs555350064	chr6:37475384-37475385	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
18	rs372592447	chr6:37475500-37475501	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs113833945	chr6:37475501-37475502	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs62408372	chr6:37475508-37475509	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	mRNA abundance
21	rs62408373	chr6:37475514-37475515	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	mRNA abundance
22	rs79951593	chr6:37475525-37475526	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs111748971	chr6:37475536-37475537	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs187485295	chr6:37475545-37475546	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs201314935	chr6:37475577-37475578	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs569063054	chr6:37475619-37475620	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs531465142	chr6:37475624-37475625	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs551181150	chr6:37475625-37475626	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs571086296	chr6:37475631-37475632	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs12205096	chr6:37475648-37475649	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs200198692	chr6:37475653-37475654	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs12212153	chr6:37475660-37475661	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs12191600	chr6:37475666-37475667	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs57491827	chr6:37475680-37475681	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs568864440	chr6:37475681-37475682	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs539577346	chr6:37475682-37475683	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs200970721	chr6:37475683-37475684	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs58759333	chr6:37475686-37475687	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs537971332	chr6:37475698-37475699	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs60653928	chr6:37475699-37475700	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs553181076	chr6:37475702-37475703	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs112066143	chr6:37475703-37475704	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs68005933	chr6:37475704-37475705	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs113206363	chr6:37475713-37475714	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs199616230	chr6:37475756-37475757	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs114970669	chr6:37475764-37475765	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs370786713	chr6:37475797-37475798	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs77639266	chr6:37475809-37475810	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs547624709	chr6:37475843-37475844	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs566212723	chr6:37475850-37475851	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:91)

Disease	PMID	Source
Follicular lymphoma	20505157	CNVD
Glioblastoma multiforme	21080181	CNVD
Ewing''s sarcoma	21437220	CNVD
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
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
Acute myeloid leukemia	20729466	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21858162	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	21448237	CNVD
Melanoma	18172304	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
Hepatocellular carcinoma	16750200	CNVD
Autism	22495311	CNVD
Cancer	16790693	CNVD
Cervical cancer	21062161	CNVD
Systemic lupus erythematosus	17503323	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Urothelial carcinoma	18382360	CNVD
Cancer	21183584	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Gastric cancer	17908304	CNVD
Metanephric adenoma	20802469	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Neuroblastoma	16790693	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Cleidocranial dysplasia	18696259	CNVD
Holoprosencephaly	21359414	CNVD
Liposarcoma	21253554	CNVD
Uveal melanoma	20484589	CNVD
Fibroblasts	20926602	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
Cancer	22183965	CNVD
Melanoma	22183965	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Lung cancer	18438408	CNVD
Glioblastoma multiforme	21138945	CNVD
Breast cancer	21364760	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Lung cancer	19153074	CNVD
Ovarian cancer	21720365	CNVD
Melanoma	21693616	CNVD
Myelofibrosis	22110671	CNVD
Mental retardation	21062444	CNVD
Breast cancer	16397240	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Osteosarcoma	21197465	CNVD
Gastric cancer	24379144	CNVD
Neuroblastoma	18923191	CNVD
Cancer	20164919	CNVD
abnormal development	18461090	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37468000-37475800	Enhancers	Thymus	Thymus
2	chr6:37468000-37477200	Enhancers	Primary T cells fromperipheralblood	blood
3	chr6:37468000-37483600	Enhancers	Fetal Thymus	thymus
4	chr6:37468200-37476000	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr6:37470600-37477000	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr6:37471000-37475800	Enhancers	Primary T cells from cord blood	blood
7	chr6:37471000-37476000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr6:37471200-37476000	Weak transcription	Dnd41	blood
9	chr6:37471200-37477800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:37471200-37483600	Weak transcription	Spleen	Spleen
11	chr6:37471400-37475800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr6:37471800-37476000	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr6:37472000-37476000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:37472200-37475800	Weak transcription	GM12878-XiMat	blood
15	chr6:37472400-37476000	Weak transcription	Fetal Kidney	kidney
16	chr6:37472800-37475800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:37472800-37476000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr6:37473800-37475400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:37473800-37482200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr6:37474400-37477000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:37474600-37475800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr6:37474600-37476200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:37474600-37476800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr6:37474800-37477400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:37475000-37475200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:37475000-37475800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr6:37475000-37476200	Enhancers	H1 Cell Line	embryonic stem cell
28	chr6:37475000-37476200	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr6:37475000-37476200	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr6:37475200-37475600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:37475200-37475800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:37475400-37475800	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr6:37475600-37476400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:37475800-37476200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr6:37475800-37476200	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr6:37475800-37476200	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr6:37475800-37476200	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr6:37475800-37476200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr6:37475800-37476200	Enhancers	Fetal Intestine Large	intestine
40	chr6:37475800-37476200	Flanking Active TSS	Thymus	Thymus
41	chr6:37475800-37476400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:37475800-37476400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr6:37475800-37476600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:37475800-37476800	Enhancers	GM12878-XiMat	blood
45	chr6:37475800-37479400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr6:37476000-37476200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr6:37476000-37476200	Enhancers	Fetal Kidney	kidney
48	chr6:37476000-37476400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr6:37476000-37476400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr6:37476000-37476400	Enhancers	Duodenum Mucosa	Duodenum

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