Variant report

Variant	esv3483548
Chromosome Location	chr9:72041232-72045830
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BACH1	chr9:72044969-72045003	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr9:72043403-72043515	GM19239	blood:	n/a	n/a
3	CTCF	chr9:72043380-72043530	GM12875	blood:	n/a	n/a
4	CTCF	chr9:72043428-72043517	GM19238	blood:	n/a	n/a
5	CTCF	chr9:72043377-72043603	K562	blood:	n/a	n/a
6	CTCF	chr9:72043360-72043510	HUVEC	blood vessel:	n/a	n/a
7	CTCF	chr9:72043423-72043514	GM12891	blood:	n/a	n/a
8	CTCF	chr9:72043378-72043557	MCF-7	breast:	n/a	n/a
9	CTCF	chr9:72043392-72043549	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr9:72043452-72043487	GM12878	blood:	n/a	n/a
11	CTCF	chr9:72043426-72043504	A549	lung:	n/a	n/a
12	CTCF	chr9:72043330-72043558	K562	blood:	n/a	n/a
13	CTCF	chr9:72043384-72043562	K562	blood:	n/a	n/a
14	CTCF	chr9:72043408-72043530	K562	blood:	n/a	n/a
15	CTCF	chr9:72043360-72043510	K562	blood:	n/a	n/a
16	CTCF	chr9:72043396-72043519	MCF-7	breast:	n/a	n/a
17	CTCF	chr9:72043362-72043531	GM12878	blood:	n/a	n/a
18	CTCF	chr9:72043400-72043534	MCF-7	breast:	n/a	n/a
19	CTCF	chr9:72043393-72043541	GM12892	blood:	n/a	n/a
20	CTCF	chr9:72043412-72043545	MCF-7	breast:	n/a	n/a
21	CTCF	chr9:72044680-72044830	GM12872	blood:	n/a	n/a
22	CTCF	chr9:72043395-72043538	MCF-7	breast:	n/a	n/a
23	CTCF	chr9:72043340-72043490	HEK293	kidney:	n/a	n/a
24	MAFK	chr9:72045749-72045945	HepG2	liver:	n/a	n/a
25	RAD21	chr9:72043340-72043585	H1-hESC	embryonic stem cell:	n/a	n/a
26	RAD21	chr9:72043367-72043489	HepG2	liver:	n/a	n/a
27	RAD21	chr9:72043336-72043662	MCF-7	breast:	n/a	n/a
28	RAD21	chr9:72043229-72043613	H1-hESC	embryonic stem cell:	n/a	n/a
29	RAD21	chr9:72043243-72043681	MCF-7	breast:	n/a	n/a
30	RAD21	chr9:72043206-72043674	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72044312..72045985-chr9:72046714..72048470,2	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-APBA1-1	chr9:72043164-72043467	ENSG00000243888
2	lnc-APBA1-1	chr9:72043544-72043637	ENSG00000243888
3	lnc-APBA1-1	chr9:72042449-72044751	NONHSAT131778

No data

Variant related genes	Relation type
ENSG00000243888	TF binding region

Extended variants
information (count: 178 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:178 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs187020351	chr9:72041236-72041237	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs546553211	chr9:72041256-72041257	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs191059862	chr9:72041283-72041284	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs529177889	chr9:72041389-72041390	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs550407272	chr9:72041390-72041391	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs73443764	chr9:72041402-72041403	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs183175707	chr9:72041408-72041409	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs186491655	chr9:72041486-72041487	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs79409110	chr9:72041538-72041539	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs78194754	chr9:72041540-72041541	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs189686807	chr9:72041599-72041600	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs534744270	chr9:72041619-72041620	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs529367815	chr9:72041691-72041692	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs553323253	chr9:72041692-72041693	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs182361581	chr9:72041695-72041696	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs536152732	chr9:72041696-72041697	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs557644565	chr9:72041759-72041760	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs575922559	chr9:72041823-72041824	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs187556365	chr9:72041824-72041825	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs535794766	chr9:72041869-72041870	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs564194771	chr9:72041910-72041911	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs577941142	chr9:72041946-72041947	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs192548177	chr9:72041963-72041964	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs140615589	chr9:72042008-72042009	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs552560790	chr9:72042048-72042049	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs371842372	chr9:72042062-72042063	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs145666633	chr9:72042063-72042064	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs562415108	chr9:72042076-72042077	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs376458925	chr9:72042088-72042089	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs1757957	chr9:72042096-72042097	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs551147468	chr9:72042181-72042182	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs570899001	chr9:72042192-72042193	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs1761284	chr9:72042193-72042194	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs183300027	chr9:72042246-72042247	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs568453747	chr9:72042272-72042273	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs188748470	chr9:72042274-72042275	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs557705932	chr9:72042279-72042280	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs1757956	chr9:72042358-72042359	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs139557173	chr9:72042366-72042367	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs374498957	chr9:72042369-72042370	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs540071642	chr9:72042374-72042375	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs17081638	chr9:72042377-72042378	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs533274962	chr9:72042378-72042379	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs148092323	chr9:72042470-72042471	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
45	rs540326276	chr9:72042500-72042501	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
46	rs561594610	chr9:72042527-72042528	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
47	rs560518180	chr9:72042572-72042573	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
48	rs549030231	chr9:72042578-72042579	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
49	rs529276573	chr9:72042590-72042591	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
50	rs549243168	chr9:72042596-72042597	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:58)

Disease	PMID	Source
Breast cancer	17133270	CNVD
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Medulloblastoma	21979893	CNVD
microdeletion syndrome	16199537	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	20164919	CNVD
Urothelial carcinoma	21177765	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Melanoma	22183965	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Cancer	16751803	CNVD
Myelofibrosis	22110671	CNVD
lymphocytic leukemia	21291569	CNVD
Leukemia	17361228	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Glioblastoma	16823260	CNVD
Leukemia	18688285	CNVD
Non-small cell lung cancer	21044232	CNVD
Brain cancer	20823417	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Astrocytoma	17387387	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Renal cell carcinoma	19461508	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Heart disease	21282601	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Lung cancer	18438408	CNVD
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute myeloid leukemia	21251322	CNVD
Breast cancer	17899364	CNVD
Mantle cell lymphoma	19029149	CNVD
Hepatocellular carcinoma	16750200	CNVD
Acute myeloid leukemia	20729466	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Oral cancer	21386901	CNVD
Epilepsy	22083797	CNVD
Glioblastoma multiforme	21750150	CNVD
Cancer	21183584	CNVD
Bipolar disorder	18458673	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72036200-72043000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr9:72036600-72082600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr9:72036800-72045200	Weak transcription	Fetal Brain Female	brain
4	chr9:72037200-72046600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr9:72037200-72048600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:72037200-72055600	Weak transcription	Fetal Lung	lung
7	chr9:72037200-72056200	Weak transcription	Fetal Muscle Leg	muscle
8	chr9:72037400-72045200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr9:72037600-72044800	Weak transcription	Fetal Stomach	stomach
10	chr9:72037600-72046600	Weak transcription	Fetal Kidney	kidney
11	chr9:72039600-72043200	Enhancers	Brain Hippocampus Middle	brain
12	chr9:72039800-72041600	Weak transcription	Liver	Liver
13	chr9:72039800-72043000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:72039800-72043400	Enhancers	Brain Angular Gyrus	brain
15	chr9:72039800-72043400	Enhancers	Brain Cingulate Gyrus	brain
16	chr9:72040000-72042000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr9:72040400-72041400	Weak transcription	Brain Anterior Caudate	brain
18	chr9:72040400-72041400	Weak transcription	Brain Substantia Nigra	brain
19	chr9:72040400-72045200	Weak transcription	Brain Germinal Matrix	brain
20	chr9:72040400-72046600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:72040600-72043600	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr9:72040600-72045000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:72040800-72042200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:72040800-72046800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr9:72040800-72057400	Weak transcription	Fetal Heart	heart
26	chr9:72041000-72043400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:72041000-72045400	Weak transcription	Ovary	ovary
28	chr9:72041200-72069600	Weak transcription	Gastric	stomach
29	chr9:72041400-72042400	Enhancers	Brain Anterior Caudate	brain
30	chr9:72041400-72043200	Enhancers	Brain Substantia Nigra	brain
31	chr9:72041600-72049400	Strong transcription	Liver	Liver
32	chr9:72041800-72045600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr9:72041800-72046600	Weak transcription	Adipose Nuclei	Adipose
34	chr9:72042000-72045400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr9:72042000-72070400	Weak transcription	Spleen	Spleen
36	chr9:72042200-72043000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr9:72042400-72043000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr9:72042400-72046600	Weak transcription	Brain Anterior Caudate	brain
39	chr9:72042600-72046200	Weak transcription	Aorta	Aorta
40	chr9:72042600-72048000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr9:72042800-72046600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr9:72042800-72063800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr9:72043000-72043400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr9:72043000-72043400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr9:72043000-72043800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr9:72043000-72046800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr9:72043200-72043400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr9:72043200-72043600	Genic enhancers	Brain Hippocampus Middle	brain
49	chr9:72043200-72063800	Weak transcription	Brain Substantia Nigra	brain
50	chr9:72043400-72044000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links