Variant report

Variant	nsv884060
Chromosome Location	chr6:30190640-30203602
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	BATF	chr6:30202214-30202520	GM12878	blood:	n/a	n/a
2	BHLHE40	chr6:30195665-30195980	GM12878	blood:	n/a	n/a
3	CEBPB	chr6:30201895-30202361	Hela-S3	cervix:	n/a	chr6:30202280-30202291
4	CEBPB	chr6:30202194-30202412	HepG2	liver:	n/a	chr6:30202280-30202291
5	CEBPB	chr6:30202205-30202406	IMR90	lung:	n/a	chr6:30202280-30202291
6	CTCF	chr6:30193180-30193330	HepG2	liver:	n/a	n/a
7	CTCF	chr6:30193465-30193504	GM13976	blood:	n/a	n/a
8	E2F4	chr6:30195213-30195222	MCF10A-Er-Src	breast:	n/a	n/a
9	EBF1	chr6:30195846-30195997	GM12878	blood:	n/a	chr6:30195936-30195947
10	EP300	chr6:30195638-30195873	GM12878	blood:	n/a	n/a
11	FOS	chr6:30202145-30202513	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr6:30202105-30202468	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr6:30202195-30202363	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr6:30202175-30202436	MCF10A-Er-Src	breast:	n/a	n/a
15	JUND	chr6:30193185-30193389	HepG2	liver:	n/a	n/a
16	MAX	chr6:30195761-30195917	HepG2	liver:	n/a	n/a
17	MEF2A	chr6:30202253-30202584	GM12878	blood:	n/a	chr6:30202505-30202519
18	MYC	chr6:30202171-30202419	MCF10A-Er-Src	breast:	n/a	n/a
19	NFIC	chr6:30195475-30196026	GM12878	blood:	n/a	n/a
20	NFYB	chr6:30195823-30196109	GM12878	blood:	n/a	chr6:30196018-30196033 chr6:30196021-30196031 chr6:30196019-30196033 chr6:30196020-30196033 chr6:30196018-30196033 chr6:30196022-30196034
21	POLR2A	chr6:30195909-30196351	GM12892	blood:	n/a	n/a
22	POLR2A	chr6:30195880-30196393	GM12891	blood:	n/a	n/a
23	POLR2A	chr6:30195764-30196309	GM12891	blood:	n/a	n/a
24	POLR2A	chr6:30195868-30196399	GM12891	blood:	n/a	n/a
25	POLR2A	chr6:30195864-30196315	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:30195795-30196374	GM12878	blood:	n/a	n/a
27	POLR2A	chr6:30195892-30196386	GM12891	blood:	n/a	n/a
28	POLR2A	chr6:30195856-30196362	GM12892	blood:	n/a	n/a
29	POLR2A	chr6:30195855-30196338	GM12891	blood:	n/a	n/a
30	POLR2A	chr6:30195883-30196292	GM12892	blood:	n/a	n/a
31	POU2F2	chr6:30195600-30196318	GM12878	blood:	n/a	n/a
32	RUNX3	chr6:30195591-30195909	GM12878	blood:	n/a	n/a
33	RUNX3	chr6:30198929-30199206	GM12878	blood:	n/a	n/a
34	RUNX3	chr6:30195520-30196032	GM12878	blood:	n/a	n/a
35	SETDB1	chr6:30191111-30191828	U2OS	brain:	n/a	n/a
36	TBP	chr6:30195763-30196116	GM12878	blood:	n/a	n/a
37	TCF7L2	chr6:30198757-30199413	HEK293	kidney:	n/a	n/a
38	USF2	chr6:30195778-30195978	GM12878	blood:	n/a	n/a
39	YY1	chr6:30195123-30195356	K562	blood:	n/a	n/a
40	YY1	chr6:30195060-30195300	H1-hESC	embryonic stem cell:	n/a	n/a
41	YY1	chr6:30195089-30195403	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30182391..30184727-chr6:30190494..30193163,2	MCF-7	breast:
2	chr6:30194307..30196564-chr6:30200875..30202443,2	K562	blood:
3	chr6:30187236..30189646-chr6:30189831..30192507,2	K562	blood:
4	chr6:30200513..30202643-chr6:30293738..30295917,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM26-2	chr6:30201816-30202045	ENSG00000242996
2	lnc-TRIM26-2	chr6:30201166-30203164	ucscGeneNc_uc003npj_2
3	lnc-TRIM26-2	chr6:30201816-30202045	ENSG00000242996
4	lnc-TRIM26-2	chr6:30202135-30202254	ENSG00000242996
5	lnc-TRIM26-2	chr6:30202135-30202227	ENSG00000242996

Variant related genes	Relation type
HCG17	TF binding region
TRIM26BP	TF binding region
ENSG00000231074	chromatin interactions
ENSG00000204599	chromatin interactions
ENSG00000270604	chromatin interactions

Extended variants
information (count: 234 )
Associated
traits (count: 110 )

Variant overlapped rSNPs/rCNVs (count:234 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs3130391	chr6:30190640-30190641	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs561585177	chr6:30190703-30190704	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs368130862	chr6:30190729-30190730	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs368377813	chr6:30190770-30190771	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs530459778	chr6:30190937-30190938	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs546857329	chr6:30191037-30191038	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs372528946	chr6:30191059-30191060	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs549138345	chr6:30191129-30191130	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs199930996	chr6:30191130-30191131	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs532459125	chr6:30191141-30191142	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs9280924	chr6:30191142-30191143	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs568779941	chr6:30191247-30191248	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
13	rs191690718	chr6:30191371-30191372	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
14	rs115838447	chr6:30194320-30194321	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs539699960	chr6:30194327-30194328	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs141186238	chr6:30194328-30194329	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs576197542	chr6:30194352-30194353	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs147385570	chr6:30194362-30194363	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs139659650	chr6:30194466-30194467	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs116252060	chr6:30194470-30194471	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs562201030	chr6:30194471-30194472	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs541208172	chr6:30194505-30194506	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs3130393	chr6:30194531-30194532	Inactive region	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs551004755	chr6:30194537-30194538	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs187044374	chr6:30194544-30194545	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs375694009	chr6:30194574-30194575	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs191966166	chr6:30194606-30194607	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs548653167	chr6:30194819-30194820	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs376245473	chr6:30194820-30194821	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs386358877	chr6:30194831-30194832	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs12660499	chr6:30194873-30194874	Inactive region	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
32	rs376445019	chr6:30194904-30194905	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs9501426	chr6:30194917-30194918	Inactive region	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs549155950	chr6:30194938-30194939	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs565773765	chr6:30194954-30194955	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs528145160	chr6:30194972-30194973	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs183537865	chr6:30194982-30194983	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs3132665	chr6:30195009-30195010	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs9501427	chr6:30195030-30195031	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs3130394	chr6:30195059-30195060	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs535820433	chr6:30195101-30195102	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs555919368	chr6:30195102-30195103	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs148937561	chr6:30195179-30195180	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs116745792	chr6:30195186-30195187	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs114898294	chr6:30195230-30195231	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs527387221	chr6:30195232-30195233	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs578167259	chr6:30195280-30195281	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs540823853	chr6:30195349-30195350	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs563717365	chr6:30195360-30195361	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs529175706	chr6:30195440-30195441	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:110)

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
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
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
Ovarian cancer	21781307	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
Cervical cancer	21062161	CNVD
Breast cancer	21785460	CNVD
Retinoblastoma	16790693	CNVD
Esophageal adenocarcinoma	18820669	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
Renal cell carcinoma	18765545	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Gastric cancer	17908304	CNVD
Metanephric adenoma	20802469	CNVD
Splenic marginal zone lymphoma	21957467	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
Myelofibrosis	22110671	CNVD
Breast cancer	16397240	CNVD
Retinoblastoma	22278416	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Systemic lupus erythematosus	20877625	CNVD
Cleidocranial dysplasia	18696259	CNVD
Holoprosencephaly	21359414	CNVD
Liposarcoma	21253554	CNVD
Uveal melanoma	20484589	CNVD
Fibroblasts	20926602	CNVD
Breast cancer	21364760	CNVD
Lung cancer	21569311	CNVD

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30187400-30191200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr6:30191200-30191400	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
3	chr6:30195000-30196200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:30195200-30195400	Enhancers	Primary T cells fromperipheralblood	blood
5	chr6:30195200-30195400	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr6:30195200-30195400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr6:30195200-30195400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:30195200-30195400	Bivalent/Poised TSS	HepG2	liver
9	chr6:30195200-30196000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:30195200-30196000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:30195200-30196000	Active TSS	GM12878-XiMat	blood
12	chr6:30195200-30196400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:30195200-30196400	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr6:30195200-30196400	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr6:30195400-30195600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr6:30195400-30195800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr6:30195400-30196000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr6:30195400-30196000	Flanking Bivalent TSS/Enh	HepG2	liver
19	chr6:30195400-30196400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:30195400-30196400	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr6:30195600-30195800	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr6:30195600-30195800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:30195600-30195800	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr6:30195600-30196400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr6:30195800-30196000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr6:30195800-30196000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
27	chr6:30195800-30196200	Enhancers	Primary T cells fromperipheralblood	blood
28	chr6:30196000-30196200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:30196000-30196200	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr6:30196000-30196200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr6:30196000-30196200	Enhancers	GM12878-XiMat	blood
32	chr6:30196000-30196400	Bivalent Enhancer	HepG2	liver
33	chr6:30197800-30198000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:30197800-30200000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:30198000-30199200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:30198000-30199600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:30198200-30199800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:30198400-30199800	Enhancers	HSMMtube	muscle
39	chr6:30198800-30199400	Enhancers	HSMM	muscle
40	chr6:30199200-30199600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:30199600-30201600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:30200000-30201400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:30201400-30202000	Enhancers	Fetal Lung	lung
44	chr6:30201400-30203000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:30201600-30202200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:30202000-30202600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
47	chr6:30202000-30202600	Flanking Active TSS	Fetal Lung	lung
48	chr6:30202200-30202600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:30202600-30202800	Enhancers	Fetal Lung	lung

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