Variant report

Variant	esv3499644
Chromosome Location	chr6:29690412-29690732
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:53)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:53 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BATF	chr6:29690673-29691059	GM12878	blood:	n/a	n/a
2	CHD2	chr6:29690678-29692171	GM12878	blood:	n/a	n/a
3	CREB1	chr6:29690590-29692094	GM12878	blood:	n/a	n/a
4	EBF1	chr6:29690575-29692170	GM12878	blood:	n/a	chr6:29690978-29690989
5	ELF1	chr6:29690688-29691524	GM12878	blood:	n/a	n/a
6	FOXM1	chr6:29690669-29691353	GM12878	blood:	n/a	n/a
7	MAZ	chr6:29690711-29692116	GM12878	blood:	n/a	n/a
8	MTA3	chr6:29690619-29691038	GM12878	blood:	n/a	n/a
9	MTA3	chr6:29690560-29692415	GM12878	blood:	n/a	n/a
10	MXI1	chr6:29690674-29691378	GM12878	blood:	n/a	n/a
11	NFIC	chr6:29690682-29691475	GM12878	blood:	n/a	n/a
12	PML	chr6:29690553-29692088	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:29690711-29694858	GM19099	blood:	n/a	n/a
14	POLR2A	chr6:29690566-29699452	GM12892	blood:	n/a	n/a
15	POLR2A	chr6:29690697-29694189	GM19193	blood:	n/a	n/a
16	POLR2A	chr6:29690663-29692513	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:29690618-29699456	GM12892	blood:	n/a	n/a
18	POLR2A	chr6:29690629-29692386	GM12892	blood:	n/a	n/a
19	POLR2A	chr6:29690594-29697494	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:29690575-29695009	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:29690708-29699614	GM18505	blood:	n/a	n/a
22	POLR2A	chr6:29690692-29694256	GM12892	blood:	n/a	n/a
23	POLR2A	chr6:29690694-29694125	GM18526	blood:	n/a	n/a
24	POLR2A	chr6:29690681-29699847	GM12878	blood:	n/a	n/a
25	POLR2A	chr6:29690698-29695012	GM18951	blood:	n/a	n/a
26	POLR2A	chr6:29690680-29694233	GM12891	blood:	n/a	n/a
27	POLR2A	chr6:29690622-29694243	GM12891	blood:	n/a	n/a
28	POLR2A	chr6:29690657-29697457	GM12892	blood:	n/a	n/a
29	POLR2A	chr6:29690658-29699867	GM12891	blood:	n/a	n/a
30	POU2F2	chr6:29690706-29691424	GM12891	blood:	n/a	n/a
31	POU2F2	chr6:29690677-29692239	GM12878	blood:	n/a	n/a
32	RELA	chr6:29690688-29691974	GM12891	blood:	n/a	n/a
33	RELA	chr6:29690701-29691888	GM19099	blood:	n/a	n/a
34	RELA	chr6:29690686-29691993	GM15510	blood:	n/a	n/a
35	RELA	chr6:29690661-29691312	GM18951	blood:	n/a	n/a
36	RFX5	chr6:29690656-29691640	HepG2	liver:	n/a	n/a
37	RFX5	chr6:29690415-29692037	SK-N-SH	brain:	n/a	n/a
38	RFX5	chr6:29690479-29691959	IMR90	lung:	n/a	n/a
39	RFX5	chr6:29690700-29691954	GM12878	blood:	n/a	n/a
40	RFX5	chr6:29690604-29692339	H1-hESC	embryonic stem cell:	n/a	n/a
41	RUNX3	chr6:29690670-29691988	GM12878	blood:	n/a	n/a
42	SP1	chr6:29690678-29691932	GM12878	blood:	n/a	n/a
43	SP1	chr6:29690643-29691292	GM12878	blood:	n/a	n/a
44	SP1	chr6:29690661-29691310	A549	lung:	n/a	n/a
45	STAT1	chr6:29690687-29691222	GM12878	blood:	n/a	n/a
46	STAT5A	chr6:29690608-29692291	GM12878	blood:	n/a	n/a
47	TAF1	chr6:29690676-29692001	GM12878	blood:	n/a	n/a
48	TBP	chr6:29690727-29691883	GM12878	blood:	n/a	n/a
49	WRNIP1	chr6:29690691-29691761	GM12878	blood:	n/a	n/a
50	YY1	chr6:29690698-29692023	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29689852..29692667-chr6:31324164..31326641,2	K562	blood:
2	chr6:29689319..29693460-chr6:29694038..29698697,5	MCF-7	breast:

No data

Variant related genes	Relation type
HLA-F	TF binding region
ENSG00000239257	chromatin interactions
ENSG00000234745	chromatin interactions
ENSG00000271581	chromatin interactions

Extended variants
information (count: 33 )
Associated
traits (count: 106 )

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs575644288	chr6:29690424-29690425	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs559440340	chr6:29690460-29690461	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs537934637	chr6:29690482-29690483	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs199603378	chr6:29690498-29690499	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs148843698	chr6:29690509-29690510	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs140490021	chr6:29690528-29690529	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
7	rs36052840	chr6:29690529-29690530	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
8	rs9258177	chr6:29690539-29690540	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	mRNA abundance
9	rs34916457	chr6:29690551-29690552	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
10	rs2517909	chr6:29690557-29690558	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
11	rs9280674	chr6:29690563-29690564	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
12	rs368651463	chr6:29690567-29690568	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
13	rs186804135	chr6:29690569-29690570	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
14	rs540548619	chr6:29690579-29690580	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
15	rs373269168	chr6:29690581-29690582	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
16	rs375959334	chr6:29690584-29690585	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
17	rs369022967	chr6:29690590-29690591	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
18	rs376230642	chr6:29690596-29690597	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
19	rs368958471	chr6:29690602-29690603	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
20	rs372574794	chr6:29690608-29690609	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
21	rs375337978	chr6:29690614-29690615	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
22	rs369855093	chr6:29690620-29690621	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
23	rs537274589	chr6:29690623-29690624	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
24	rs549958736	chr6:29690626-29690627	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
25	rs574611152	chr6:29690641-29690642	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
26	rs540011140	chr6:29690652-29690653	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
27	rs55875967	chr6:29690658-29690659	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
28	rs143621629	chr6:29690662-29690663	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	mRNA abundance
29	rs9258183	chr6:29690669-29690670	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
30	rs9258184	chr6:29690671-29690672	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
31	rs3998799	chr6:29690694-29690695	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
32	rs114795943	chr6:29690715-29690716	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
33	rs536529663	chr6:29690721-29690722	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:106)

Disease	PMID	Source
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
Acute lymphoblastic leukemia	20435627	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21858162	CNVD
Lung cancer	18438408	CNVD
Ewing''s sarcoma	17952124	CNVD
Gastric cancer	16891809	CNVD
Ovarian cancer	21781307	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Autism	21448237	CNVD
Cancer	20164919	CNVD
Melanoma	18172304	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
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
Chronic lymphocytic leukemia	21546498	CNVD
Congenital anomalies of the kidney and urinary tract	18694510	CNVD
Nasopharyngeal cancer	22815911	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	21115979	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	17133270	CNVD
Autism	22495311	CNVD
Cancer	16790693	CNVD
Breast cancer	22032731	CNVD
Cervical cancer	21062161	CNVD
Breast cancer	21785460	CNVD
Retinoblastoma	16790693	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Systemic lupus erythematosus	17503323	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
T-cell lymphomas	19863542	CNVD
Urothelial carcinoma	18382360	CNVD
Cancer	21183584	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
Renal cell carcinoma	18765545	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Gastric cancer	17908304	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	16397240	CNVD
Metanephric adenoma	20802469	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	21364760	CNVD
Schizophrenia	19571809	CNVD
Schizophrenia	19571808	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Neuroblastoma	16790693	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
abnormal development	18461090	CNVD
Breast cancer	21509527	CNVD
Melanoma	17363583	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29664000-29690600	Weak transcription	Right Atrium	heart
2	chr6:29688600-29690800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:29689400-29690800	Weak transcription	Spleen	Spleen
4	chr6:29689600-29690600	Enhancers	Primary B cells from cord blood	blood
5	chr6:29690000-29690600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr6:29690000-29690600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:29690000-29691200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
8	chr6:29690000-29692000	Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr6:29690000-29692000	Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr6:29690000-29692200	Active TSS	GM12878-XiMat	blood
11	chr6:29690200-29690600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:29690200-29690600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:29690200-29690600	Active TSS	Monocytes-CD14+_RO01746	blood
14	chr6:29690200-29690800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr6:29690200-29691200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr6:29690200-29692000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
17	chr6:29690400-29690600	Enhancers	Primary T cells from cord blood	blood
18	chr6:29690400-29690600	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr6:29690400-29690600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:29690400-29690600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:29690400-29690600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr6:29690400-29690600	Active TSS	Adipose Nuclei	Adipose
23	chr6:29690400-29690800	Flanking Active TSS	Primary B cells from peripheral blood	blood
24	chr6:29690400-29691000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:29690400-29691200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:29690400-29691800	Bivalent/Poised TSS	Primary neutrophils fromperipheralblood	blood
27	chr6:29690400-29692000	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr6:29690400-29692000	Active TSS	Primary T cells fromperipheralblood	blood
29	chr6:29690400-29692000	Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr6:29690400-29692000	Active TSS	Brain Anterior Caudate	brain
31	chr6:29690400-29692000	Active TSS	Duodenum Mucosa	Duodenum
32	chr6:29690400-29692600	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr6:29690400-29692800	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr6:29690600-29690800	Active TSS	Primary hematopoietic stem cells	blood
35	chr6:29690600-29690800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:29690600-29690800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:29690600-29690800	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr6:29690600-29690800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
39	chr6:29690600-29690800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
40	chr6:29690600-29690800	Bivalent Enhancer	Fetal Thymus	thymus
41	chr6:29690600-29690800	Bivalent Enhancer	HepG2	liver
42	chr6:29690600-29690800	Flanking Bivalent TSS/Enh	NHDF-Ad	bronchial
43	chr6:29690600-29691000	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr6:29690600-29691000	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr6:29690600-29691000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
46	chr6:29690600-29691000	Active TSS	Psoas Muscle	Psoas
47	chr6:29690600-29691000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
48	chr6:29690600-29691000	Flanking Active TSS	Thymus	Thymus
49	chr6:29690600-29691000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr6:29690600-29691000	Flanking Active TSS	NHEK	skin

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