Variant report

Variant	esv3473791
Chromosome Location	chr6:5692573-5707035
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	ATF1	chr6:5701673-5701868	K562	blood:	n/a	n/a
2	CEBPB	chr6:5695346-5695786	IMR90	lung:	n/a	n/a
3	CTCF	chr6:5706780-5706930	HEEpiC	esophagus:	n/a	n/a
4	CTCF	chr6:5706960-5707110	NHDF-neo	bronchial:	n/a	n/a
5	CTCF	chr6:5698183-5698236	GM13976	blood:	n/a	n/a
6	CTCF	chr6:5706860-5707010	AG04449	skin:	n/a	n/a
7	EP300	chr6:5698502-5699006	ECC-1	luminal epithelium:	n/a	n/a
8	EP300	chr6:5698373-5699736	ECC-1	luminal epithelium:	n/a	n/a
9	FOS	chr6:5697805-5697857	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr6:5695644-5695709	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr6:5695540-5695744	MCF10A-Er-Src	breast:	n/a	chr6:5695642-5695653 chr6:5695643-5695652
12	FOS	chr6:5695446-5695912	HUVEC	blood vessel:	n/a	chr6:5695642-5695653 chr6:5695643-5695652
13	FOS	chr6:5695481-5695886	MCF10A-Er-Src	breast:	n/a	chr6:5695642-5695653 chr6:5695643-5695652
14	FOXP2	chr6:5695394-5695797	SK-N-MC	brain:	n/a	n/a
15	JUN	chr6:5697833-5697862	HepG2	liver:	n/a	n/a
16	JUND	chr6:5701731-5701779	HepG2	liver:	n/a	chr6:5701745-5701754
17	KAP1	chr6:5695583-5695897	U2OS	brain:	n/a	chr6:5695601-5695609
18	MAFK	chr6:5695195-5695322	HepG2	liver:	n/a	n/a
19	MAFK	chr6:5695168-5695364	HepG2	liver:	n/a	n/a
20	MAFK	chr6:5695644-5696023	IMR90	lung:	n/a	n/a
21	MAFK	chr6:5696330-5696432	HepG2	liver:	n/a	chr6:5696398-5696413
22	MAFK	chr6:5696302-5696488	K562	blood:	n/a	chr6:5696398-5696413
23	MAFK	chr6:5696384-5696408	HepG2	liver:	n/a	n/a
24	MAFK	chr6:5696225-5696402	IMR90	lung:	n/a	n/a
25	MXI1	chr6:5695302-5695790	IMR90	lung:	n/a	n/a
26	MYC	chr6:5695488-5695758	MCF10A-Er-Src	breast:	n/a	chr6:5695644-5695653
27	MYC	chr6:5706445-5706541	H1-hESC	embryonic stem cell:	n/a	n/a
28	MYC	chr6:5695545-5695784	MCF10A-Er-Src	breast:	n/a	chr6:5695644-5695653
29	MYC	chr6:5695540-5695756	HUVEC	blood vessel:	n/a	chr6:5695644-5695653
30	MYC	chr6:5699223-5699237	H1-hESC	embryonic stem cell:	n/a	n/a
31	NFIC	chr6:5699305-5699725	ECC-1	luminal epithelium:	n/a	n/a
32	NFIC	chr6:5698456-5699217	ECC-1	luminal epithelium:	n/a	n/a
33	NFIC	chr6:5698517-5699265	ECC-1	luminal epithelium:	n/a	n/a
34	NRF1	chr6:5695188-5695194	K562	blood:	n/a	n/a
35	PAX5	chr6:5700945-5701172	GM12878	blood:	n/a	n/a
36	PAX5	chr6:5700918-5701217	GM12878	blood:	n/a	n/a
37	POLR2A	chr6:5695421-5695909	U87	brain:	n/a	n/a
38	POLR2A	chr6:5695337-5695899	U87	brain:	n/a	n/a
39	POLR2A	chr6:5695443-5695863	SK-N-MC	brain:	n/a	n/a
40	POLR2A	chr6:5698492-5698598	MCF-7	breast:	n/a	n/a
41	POLR2A	chr6:5705529-5705736	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:5705740-5705927	GM12878	blood:	n/a	n/a
43	POLR2A	chr6:5701349-5701385	Gliobla	brain:	n/a	n/a
44	POLR2A	chr6:5695443-5695613	ProgFib	skin:	n/a	n/a
45	RAD21	chr6:5695558-5695814	IMR90	lung:	n/a	n/a
46	RCOR1	chr6:5698233-5698373	K562	blood:	n/a	n/a
47	RFX5	chr6:5695261-5696387	IMR90	lung:	n/a	n/a
48	RUNX3	chr6:5695490-5695870	GM12878	blood:	n/a	n/a
49	SETDB1	chr6:5695433-5695851	U2OS	brain:	n/a	n/a
50	SMC3	chr6:5695999-5696004	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:5704687..5707322-chr6:5708946..5711451,2	K562	blood:
2	chr6:5693144..5695686-chr6:5698907..5701640,2	K562	blood:
3	chr6:5692733..5695686-chr6:5700140..5701743,2	K562	blood:
4	chr6:5704009..5705520-chr6:5708074..5709705,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NRN1-7	chr6:5695115-5695241	ENSG00000270174.1
2	lnc-NRN1-7	chr6:5695378-5695505	ENSG00000270174.1

Variant related genes	Relation type
ENSG00000270174	TF binding region
ENSG00000270174	chromatin interactions

Extended variants
information (count: 561 )
Associated
traits (count: 99 )

Variant overlapped rSNPs/rCNVs (count:561 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs368724285	chr6:5692606-5692607	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
2	rs575594439	chr6:5692652-5692653	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs546155477	chr6:5692653-5692654	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs192565959	chr6:5692657-5692658	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs113910512	chr6:5692764-5692765	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs78413837	chr6:5692780-5692781	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs540301992	chr6:5692782-5692783	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs557951545	chr6:5692800-5692801	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs184379536	chr6:5692819-5692820	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
10	rs529406709	chr6:5692820-5692821	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
11	rs565679047	chr6:5692831-5692832	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs189079895	chr6:5692888-5692889	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
13	rs138423393	chr6:5692934-5692935	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
14	rs77419181	chr6:5692939-5692940	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
15	rs559047238	chr6:5692945-5692946	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
16	rs140292783	chr6:5692970-5692971	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs534733116	chr6:5692971-5692972	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
18	rs760674	chr6:5692989-5692990	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs760675	chr6:5693007-5693008	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
20	rs557093189	chr6:5693019-5693020	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
21	rs145190899	chr6:5693021-5693022	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
22	rs557000624	chr6:5693023-5693024	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs575479322	chr6:5693075-5693076	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
24	rs573997798	chr6:5693085-5693086	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
25	rs182179662	chr6:5693090-5693091	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
26	rs137907740	chr6:5693105-5693106	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
27	rs367842390	chr6:5693152-5693153	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs373470391	chr6:5693160-5693161	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
29	rs542911267	chr6:5693182-5693183	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs371608810	chr6:5693211-5693212	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs540339108	chr6:5693244-5693245	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs78829457	chr6:5693275-5693276	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs376907833	chr6:5693331-5693332	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs574200156	chr6:5693375-5693376	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs367913306	chr6:5693408-5693409	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs143294454	chr6:5693429-5693430	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs116737052	chr6:5693454-5693455	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs143050777	chr6:5693540-5693541	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs186310648	chr6:5693633-5693634	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs144408750	chr6:5693644-5693645	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs528080636	chr6:5693659-5693660	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs79872604	chr6:5693660-5693661	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs568137476	chr6:5693672-5693673	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs529110643	chr6:5693685-5693686	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs148345209	chr6:5693692-5693693	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs112731660	chr6:5693700-5693701	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs550765987	chr6:5693702-5693703	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs535534749	chr6:5693751-5693752	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs534275169	chr6:5693772-5693773	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs189975525	chr6:5693782-5693783	Weak transcription Genic enhancers Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:99)

Disease	PMID	Source
Developmental delay	19490664	CNVD
Cancer	21183584	CNVD
Multiple Epiphyseal Dysplasia	20877625	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Glaucoma	18694899	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Prostate cancer	16573809	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	17603634	CNVD
Cancer	20164920	CNVD
Colorectal cancer	21297112	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
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
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Prostate cancer	18632612	CNVD
Myelodysplastic syndrome	21251322	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Breast cancer	21858162	CNVD
Lung cancer	18438408	CNVD
Bladder cancer	21909424	CNVD
Multiple myeloma	17550852	CNVD
Ewing''s sarcoma	17952124	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Gastric cancer	16891809	CNVD
Ovarian cancer	21781307	CNVD
Autism	22495311	CNVD
Autism	21448237	CNVD
Cancer	20164919	CNVD
Melanoma	18172304	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Breast cancer	22844521	CNVD
HIV/AIDS	22844521	CNVD
Ovarian cancer	22844521	CNVD
Prostate cancer	22844521	CNVD
Psoriasis	22844521	CNVD
Rheumatoid arthritis	22844521	CNVD
Sclerosis systemic	22844521	CNVD
Systemic lupus erythematosus	22844521	CNVD
Breast cancer	22522925	CNVD
Breast cancer	21552322	CNVD
Immune disease	21076436	CNVD
Autoimmune disease	19135723	CNVD
Systemic lupus erythematosus	17953491	CNVD
Recurrent Infections	22737222	CNVD
Systemic lupus erythematosus	21904924	CNVD
Ependymoma	19289631	CNVD
small cell lung cancer	20016488	CNVD
Gestational infection	22844521	CNVD
Head circumference	22844521	CNVD
Infertility	22844521	CNVD
Recurrent birth weight diabetes	22844521	CNVD
Obesity	22844521	CNVD
Recurrent pregnancy loss	22844521	CNVD
Intellectual disability	21811512	CNVD
Congenital anomalies of the kidney and urinary tract	18694510	CNVD
Nasopharyngeal cancer	22815911	CNVD
dysmorphism	22105932	CNVD
psychomotor delay	22105932	CNVD
Ovarian cancer	19193619	CNVD
Osteosarcoma	16790693	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	21115979	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Pancreatic cancer	17952125	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Breast cancer	21364760	CNVD

Chromatin state (count:240 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5672200-5705800	Weak transcription	Thymus	Thymus
2	chr6:5673800-5701200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr6:5673800-5709800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:5678000-5709400	Weak transcription	Pancreas	Pancrea
5	chr6:5678200-5694000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:5678400-5693400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:5680600-5695400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr6:5680800-5695000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr6:5681800-5695000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr6:5682200-5693200	Weak transcription	Primary T cells from cord blood	blood
11	chr6:5682400-5695200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr6:5682400-5695400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:5684600-5695400	Weak transcription	Fetal Stomach	stomach
14	chr6:5684800-5696000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:5684800-5706000	Weak transcription	Ovary	ovary
16	chr6:5685000-5695400	Weak transcription	HSMMtube	muscle
17	chr6:5685000-5698600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:5691400-5698200	Weak transcription	Spleen	Spleen
19	chr6:5692000-5693200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:5692400-5693000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
21	chr6:5692600-5695000	Weak transcription	Dnd41	blood
22	chr6:5692800-5701400	Weak transcription	Right Atrium	heart
23	chr6:5693000-5696000	Weak transcription	Fetal Intestine Small	intestine
24	chr6:5693200-5694200	Genic enhancers	Primary T cells from cord blood	blood
25	chr6:5693400-5694400	Enhancers	Fetal Thymus	thymus
26	chr6:5693400-5695200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:5693800-5694000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:5694000-5694200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:5694000-5694400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
30	chr6:5694200-5694600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:5694200-5695000	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr6:5694200-5695400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:5694200-5695800	Weak transcription	NH-A	brain
34	chr6:5694400-5694800	Weak transcription	Fetal Thymus	thymus
35	chr6:5694400-5695000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:5694800-5696400	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr6:5694800-5696400	Enhancers	Fetal Thymus	thymus
38	chr6:5695000-5695200	Enhancers	Primary T cells from cord blood	blood
39	chr6:5695000-5695200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:5695000-5695200	Enhancers	NHDF-Ad	bronchial
41	chr6:5695000-5695400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:5695000-5695800	Enhancers	Primary T cells fromperipheralblood	blood
43	chr6:5695000-5696200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr6:5695000-5696400	Enhancers	Dnd41	blood
45	chr6:5695000-5696600	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr6:5695200-5695400	Enhancers	Osteobl	bone
47	chr6:5695200-5695600	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr6:5695200-5696200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:5695200-5696200	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr6:5695200-5696200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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