Variant report

Variant	esv1005947
Chromosome Location	chr10:49659234-49660340
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:49659968-49660014	IMR90	lung:	n/a	n/a
2	POLR2A	chr10:49659688-49660327	U87	brain:	n/a	n/a
3	POLR2A	chr10:49659188-49659616	U87	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:49659559-49659609	T-47D	breast:	n/a
2	chr10:49659559-49659609	SKMC	muscle:	n/a
3	chr10:49659559-49659609	HNPCEpiC	eye:	n/a
4	chr10:49659559-49659609	ECC-1	luminal epithelium:	n/a
5	chr10:49659559-49659609	HRE	kidney:	n/a
6	chr10:49659559-49659609	GM19239	blood:	n/a
7	chr10:49659559-49659609	IMR90	lung:	fetal
8	chr10:49659559-49659609	BJ	skin:	n/a
9	chr10:49659559-49659609	Hela-S3	cervix:	n/a
10	chr10:49659559-49659609	HEK293	kidney:	embryo
11	chr10:49659559-49659609	SAEC	small airway:	n/a
12	chr10:49659559-49659609	HIPEpiC	eye:	n/a
13	chr10:49659559-49659609	MCF10A-Er-Src	breast:	n/a
14	chr10:49659559-49659609	HMEC	breast:	n/a
15	chr10:49659559-49659609	HepG2	liver:	n/a
16	chr10:49659559-49659609	GM06990	blood:	n/a
17	chr10:49659559-49659609	ovcar-3	ovarian:	n/a
18	chr10:49659559-49659609	NT2-D1	testis:	n/a
19	chr10:49659559-49659609	LNCaP	prostate:	n/a
20	chr10:49659559-49659609	PrEC	prostate:	n/a
21	chr10:49659559-49659609	Jurkat	blood:	n/a
22	chr10:49659559-49659609	SK-N-SH	brain:	n/a
23	chr10:49659559-49659609	ProgFib	skin:	n/a
24	chr10:49659559-49659609	A549	lung:	n/a
25	chr10:49659559-49659609	Hepatocyte	liver:	n/a
26	chr10:49659559-49659609	HCF	heart:	n/a
27	chr10:49659559-49659609	AG09319	gingival:	n/a
28	chr10:49659559-49659609	GM12891	blood:	n/a
29	chr10:49659559-49659609	H1-hESC	embryonic stem cell:	embryo
30	chr10:49659559-49659609	CMK	blood:	n/a
31	chr10:49659559-49659609	PFSK-1	brain:	n/a
32	chr10:49659559-49659609	HRPEpiC	eye:	n/a
33	chr10:49659559-49659609	Caco-2	colon:	n/a
34	chr10:49659559-49659609	K562	blood:	n/a
35	chr10:49659559-49659609	HAEpiC	amniotic membrane:	n/a
36	chr10:49659559-49659609	SK-N-SH_RA	brain:	n/a
37	chr10:49659559-49659609	NB4	blood:	n/a
38	chr10:49659559-49659609	RPTEC	kidney:	n/a
39	chr10:49659559-49659609	AG04450	lung:	fetal
40	chr10:49659559-49659609	NHBE	bronchial:	n/a
41	chr10:49659559-49659609	HPAEpiC	pulmonary alveolar:	n/a
42	chr10:49659559-49659609	AoSMC	blood vessel:	n/a
43	chr10:49659559-49659609	NHDF-neo	bronchial:	n/a
44	chr10:49659559-49659609	AG10803	skin:	n/a
45	chr10:49659559-49659609	GM12892	blood:	n/a
46	chr10:49659559-49659609	AG09309	skin:	n/a
47	chr10:49659559-49659609	HL-60	blood:	n/a
48	chr10:49659559-49659609	BE2_C	brain:	n/a
49	chr10:49659559-49659609	NH-A	brain:	n/a
50	chr10:49659559-49659609	HCT-116	colon:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:49656960..49659502-chr10:49666267..49668119,2	MCF-7	breast:
2	chr10:49647174..49649169-chr10:49659703..49661995,2	MCF-7	breast:
3	chr10:49660046..49662024-chr10:49725429..49726985,2	K562	blood:
4	chr10:49607978..49609733-chr10:49660029..49662465,2	K562	blood:
5	chr10:49659900..49662821-chr10:49704182..49706648,2	K562	blood:

No data

Variant related genes	Relation type
ARHGAP22	TF binding region
ARHGAP22	CpG island
ENSG00000107643	chromatin interactions

Extended variants
information (count: 45 )
Associated
traits (count: 71 )

Variant overlapped rSNPs/rCNVs (count:45 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs565131908	chr10:49659239-49659240	Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs543459171	chr10:49659316-49659317	Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs1867587	chr10:49659351-49659352	Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs547108740	chr10:49659360-49659361	Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs562523564	chr10:49659373-49659374	Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs562318726	chr10:49659399-49659400	Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs529659252	chr10:49659411-49659412	Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs80068542	chr10:49659426-49659427	Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs559819504	chr10:49659440-49659441	Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs35864672	chr10:49659454-49659455	Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs376521601	chr10:49659487-49659488	Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs527431696	chr10:49659501-49659502	Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs10776601	chr10:49659559-49659560	Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
14	rs3827681	chr10:49659637-49659638	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
15	rs72796303	chr10:49659644-49659645	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs551276681	chr10:49659667-49659668	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs34510194	chr10:49659686-49659687	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs115507432	chr10:49659691-49659692	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs536654898	chr10:49659727-49659728	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs180780062	chr10:49659755-49659756	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs149120007	chr10:49659759-49659760	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs377065667	chr10:49659760-49659761	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs186019715	chr10:49659763-49659764	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs3813863	chr10:49659772-49659773	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs548095885	chr10:49659785-49659786	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs567884798	chr10:49659790-49659791	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs534328462	chr10:49659822-49659823	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs80335242	chr10:49659842-49659843	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs3813864	chr10:49659843-49659844	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs191169735	chr10:49659955-49659956	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs183164289	chr10:49659970-49659971	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs11101325	chr10:49660001-49660002	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
33	rs541422759	chr10:49660053-49660054	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs558456929	chr10:49660089-49660090	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs559758589	chr10:49660109-49660110	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs74830708	chr10:49660118-49660119	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs113987287	chr10:49660137-49660138	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs545910511	chr10:49660154-49660155	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs565308295	chr10:49660217-49660218	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs370777833	chr10:49660239-49660240	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs532755347	chr10:49660266-49660267	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs550952776	chr10:49660283-49660284	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs10857570	chr10:49660296-49660297	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs187944372	chr10:49660299-49660300	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs548591183	chr10:49660308-49660309	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:71)

Disease	PMID	Source
Pancreatic endocrine tumor	17639061	CNVD
Gastric cancer	17908304	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	CNVD
Melanoma	18172304	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Ewing''s sarcoma	17952124	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	20724749	CNVD
Autism	22495311	CNVD
Esophageal cancer	21851588	CNVD
Prostate cancer	18632612	CNVD
Autism	18414403	CNVD
Cockayne syndrome	18421352	CNVD
Glioblastoma	16823260	CNVD
Medulloblastoma	16968546	CNVD
Neuroblastoma	17533364	CNVD
Cancer	21183584	CNVD
T-cell lymphomas	19863542	CNVD
Testicular germ cell tumor	18059402	CNVD
Squamous cell cancer	21044232	CNVD
Glioma	21971842	CNVD
Cancer	21637783	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Hirschsprung''s Disease	21712996	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Obesity	21956041	CNVD
Renal cell carcinoma	18765545	CNVD
Developmental delay	21948486	CNVD
Dysmorphic features	21948486	CNVD
Epilepsy	21948486	CNVD
Breast cancer	21785460	CNVD
Intellectual disability	21948486	CNVD
Schizophrenia	23813976	CNVD
Acute myeloid leukemia	19651601	CNVD
Breast cancer	20409316	CNVD
Breast cancer	21990379	CNVD
Myelofibrosis	22110671	CNVD
Rett syndrome	21593744	CNVD
Glioblastoma multiforme	22286061	CNVD
Neuroblastoma	21899760	CNVD
Intellectual disability	22045946	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Autism	21948486	CNVD
cleft palate	21948486	CNVD
Encephalopathy	21948486	CNVD
Lung cancer	18438408	CNVD
T-cell primary immunodeficiency	21948486	CNVD
Autism	22543975	CNVD
Breast cancer	21364760	CNVD
Developmental delay	21147756	CNVD
small cell lung cancer	20016488	CNVD
skeletal anomalies	21948486	CNVD
speech delay	21948486	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49612000-49664200	Weak transcription	Thymus	Thymus
2	chr10:49612800-49660200	Weak transcription	Aorta	Aorta
3	chr10:49619000-49664200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr10:49621400-49664400	Weak transcription	Brain Angular Gyrus	brain
5	chr10:49624600-49664800	Weak transcription	Gastric	stomach
6	chr10:49626600-49664400	Weak transcription	Spleen	Spleen
7	chr10:49644200-49664400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr10:49644600-49660400	Weak transcription	Brain Anterior Caudate	brain
9	chr10:49647800-49663000	Weak transcription	NHEK	skin
10	chr10:49647800-49664400	Weak transcription	Fetal Intestine Small	intestine
11	chr10:49648000-49664400	Weak transcription	Right Atrium	heart
12	chr10:49650600-49664000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr10:49652000-49673000	Weak transcription	HMEC	breast
14	chr10:49652600-49664200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr10:49653000-49660400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr10:49653000-49673600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr10:49653200-49662400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr10:49653200-49663600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr10:49653400-49659400	Weak transcription	Pancreas	Pancrea
20	chr10:49653600-49662400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr10:49653600-49664400	Weak transcription	Esophagus	oesophagus
22	chr10:49653600-49664600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr10:49655200-49677800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr10:49656000-49661800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr10:49656600-49662200	Strong transcription	Primary hematopoietic stem cells	blood
26	chr10:49656800-49662000	Strong transcription	Fetal Stomach	stomach
27	chr10:49657200-49661200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr10:49657400-49659600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr10:49657600-49660800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr10:49657600-49660800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr10:49657600-49662000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr10:49657600-49662600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr10:49657800-49662200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr10:49657800-49664400	Strong transcription	NHLF	lung
35	chr10:49657800-49677600	Weak transcription	HSMMtube	muscle
36	chr10:49658000-49660400	Weak transcription	K562	blood
37	chr10:49658000-49661800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr10:49658000-49664400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr10:49658200-49660400	Weak transcription	HSMM	muscle
40	chr10:49658200-49660400	Weak transcription	NH-A	brain
41	chr10:49658200-49663400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr10:49658200-49664200	Weak transcription	Adipose Nuclei	Adipose
43	chr10:49658200-49664200	Weak transcription	HUVEC	blood vessel
44	chr10:49658200-49664400	Weak transcription	Right Ventricle	heart
45	chr10:49658400-49662000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr10:49658400-49662000	Strong transcription	Brain Hippocampus Middle	brain
47	chr10:49658400-49662400	Strong transcription	Osteobl	bone
48	chr10:49658600-49660800	Strong transcription	Brain Substantia Nigra	brain
49	chr10:49658600-49661000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr10:49658600-49662400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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