Variant report

Variant	esv3349281
Chromosome Location	chrY:6077640-6406768
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:623)
CpG islands
(count:1159)
Chromatin interactive
region (count:0)
LncRNA
region (count:78)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:623 , 50 per page) page: 1 2 3 4 5 6 7 ... 13

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chrY:6368607-6368683	GM20000	blood:	n/a	n/a
2	CTCF	chrY:6198527-6198598	GM10248	blood:	n/a	n/a
3	CTCF	chrY:6277587-6277720	LNCaP	prostate:	n/a	n/a
4	CTCF	chrY:6380171-6380269	GM10266	blood:	n/a	n/a
5	CTCF	chrY:6236168-6236255	LNCaP	prostate:	n/a	n/a
6	CTCF	chrY:6227994-6228130	LNCaP	prostate:	n/a	n/a
7	CTCF	chrY:6083499-6083565	GM10248	blood:	n/a	n/a
8	CTCF	chrY:6225839-6225901	Medullo	brain:	n/a	n/a
9	CTCF	chrY:6286302-6286361	Medullo	brain:	n/a	n/a
10	CTCF	chrY:6309782-6309866	HepG2	liver:	n/a	n/a
11	CTCF	chrY:6184459-6184591	GM10266	blood:	n/a	n/a
12	CTCF	chrY:6245870-6245937	Medullo	brain:	n/a	n/a
13	CTCF	chrY:6388227-6388251	A549	lung:	n/a	n/a
14	CTCF	chrY:6321768-6321849	LNCaP	prostate:	n/a	n/a
15	CTCF	chrY:6169796-6169818	GM10266	blood:	n/a	n/a
16	CTCF	chrY:6380583-6380662	Medullo	brain:	n/a	n/a
17	CTCF	chrY:6238746-6238771	A549	lung:	n/a	n/a
18	CTCF	chrY:6263131-6263161	GM19239	blood:	n/a	n/a
19	CTCF	chrY:6164783-6164852	Medullo	brain:	n/a	n/a
20	CTCF	chrY:6360975-6360993	ProgFib	skin:	n/a	n/a
21	CTCF	chrY:6284364-6284444	LNCaP	prostate:	n/a	n/a
22	CTCF	chrY:6242066-6242088	GM12891	blood:	n/a	n/a
23	CTCF	chrY:6275059-6275110	LNCaP	prostate:	n/a	n/a
24	CTCF	chrY:6098606-6098664	GM10266	blood:	n/a	n/a
25	CTCF	chrY:6300687-6300724	LNCaP	prostate:	n/a	n/a
26	CTCF	chrY:6325798-6325891	LNCaP	prostate:	n/a	n/a
27	CTCF	chrY:6186932-6186942	LNCaP	prostate:	n/a	n/a
28	CTCF	chrY:6195742-6195743	GM10248	blood:	n/a	n/a
29	CTCF	chrY:6329650-6329741	LNCaP	prostate:	n/a	n/a
30	CTCF	chrY:6091481-6091500	ProgFib	skin:	n/a	n/a
31	CTCF	chrY:6107019-6107085	GM10266	blood:	n/a	n/a
32	CTCF	chrY:6105105-6105130	GM10248	blood:	n/a	n/a
33	CTCF	chrY:6195759-6195827	HepG2	liver:	n/a	n/a
34	CTCF	chrY:6195753-6195912	GM10248	blood:	n/a	n/a
35	CTCF	chrY:6079552-6079701	GM10266	blood:	n/a	n/a
36	CTCF	chrY:6352413-6352509	HepG2	liver:	n/a	n/a
37	CTCF	chrY:6388251-6388320	GM20000	blood:	n/a	n/a
38	CTCF	chrY:6193433-6193524	GM10248	blood:	n/a	n/a
39	CTCF	chrY:6192044-6192088	GM10248	blood:	n/a	n/a
40	CTCF	chrY:6273221-6273305	LNCaP	prostate:	n/a	n/a
41	CTCF	chrY:6358548-6358597	LNCaP	prostate:	n/a	n/a
42	CTCF	chrY:6239109-6239220	LNCaP	prostate:	n/a	n/a
43	CTCF	chrY:6169340-6169431	GM20000	blood:	n/a	n/a
44	CTCF	chrY:6209288-6209332	ProgFib	skin:	n/a	n/a
45	CTCF	chrY:6195586-6195627	GM20000	blood:	n/a	n/a
46	CTCF	chrY:6185775-6185838	LNCaP	prostate:	n/a	n/a
47	CTCF	chrY:6263554-6263609	GM10248	blood:	n/a	n/a
48	CTCF	chrY:6260283-6260388	GM20000	blood:	n/a	n/a
49	CTCF	chrY:6256809-6256966	Pancreas_OC	pancreas:	n/a	n/a
50	CTCF	chrY:6379792-6379845	GM10248	blood:	n/a	n/a

(count:1159 , 50 per page) page: 1 2 3 4 5 6 7 ... 24

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chrY:6114379-6114429	MCF10A-Er-Src	breast:	n/a
2	chrY:6388486-6388536	GM12878	blood:	n/a
3	chrY:6114379-6114429	LNCaP	prostate:	n/a
4	chrY:6114255-6114305	GM12891	blood:	n/a
5	chrY:6133838-6133888	SKMC	muscle:	n/a
6	chrY:6172428-6172478	Hela-S3	cervix:	n/a
7	chrY:6114379-6114429	K562	blood:	n/a
8	chrY:6137453-6137503	HAEpiC	amniotic membrane:	n/a
9	chrY:6114379-6114429	HUVEC	blood vessel:	n/a
10	chrY:6172428-6172478	Caco-2	colon:	n/a
11	chrY:6388486-6388536	AoSMC	blood vessel:	n/a
12	chrY:6114255-6114305	HCT-116	colon:	n/a
13	chrY:6137453-6137503	Hepatocyte	liver:	n/a
14	chrY:6131007-6131057	SK-N-MC	brain:	n/a
15	chrY:6134650-6134700	HPAEpiC	pulmonary alveolar:	n/a
16	chrY:6114255-6114305	RPTEC	kidney:	n/a
17	chrY:6388486-6388536	HUVEC	blood vessel:	n/a
18	chrY:6133740-6133790	ProgFib	skin:	n/a
19	chrY:6114255-6114305	SKMC	muscle:	n/a
20	chrY:6388486-6388536	HEK293	kidney:	embryo
21	chrY:6172428-6172478	HCPEpiC	choroid plexus:	n/a
22	chrY:6312218-6312268	HEEpiC	esophagus:	n/a
23	chrY:6134650-6134700	U87	brain:	n/a
24	chrY:6172428-6172478	HL-60	blood:	n/a
25	chrY:6136711-6136761	ECC-1	luminal epithelium:	n/a
26	chrY:6131963-6132013	SAEC	small airway:	n/a
27	chrY:6114379-6114429	PANC-1	pancreas:	n/a
28	chrY:6133838-6133888	GM12891	blood:	n/a
29	chrY:6312218-6312268	AG04450	lung:	fetal
30	chrY:6134650-6134700	AG09309	skin:	n/a
31	chrY:6134650-6134700	IMR90	lung:	fetal
32	chrY:6113261-6113311	GM12878	blood:	n/a
33	chrY:6137453-6137503	ovcar-3	ovarian:	n/a
34	chrY:6341961-6342011	PANC-1	pancreas:	n/a
35	chrY:6172783-6172833	HRCEpiC	kidney:	n/a
36	chrY:6173766-6173816	PFSK-1	brain:	n/a
37	chrY:6117321-6117371	Hela-S3	cervix:	n/a
38	chrY:6263841-6263891	U87	brain:	n/a
39	chrY:6114379-6114429	AG09309	skin:	n/a
40	chrY:6136711-6136761	NH-A	brain:	n/a
41	chrY:6173766-6173816	K562	blood:	n/a
42	chrY:6131007-6131057	AG04450	lung:	fetal
43	chrY:6131963-6132013	Hela-S3	cervix:	n/a
44	chrY:6133838-6133888	NB4	blood:	n/a
45	chrY:6113261-6113311	HIPEpiC	eye:	n/a
46	chrY:6263841-6263891	Hela-S3	cervix:	n/a
47	chrY:6388486-6388536	HepG2	liver:	n/a
48	chrY:6137453-6137503	GM19239	blood:	n/a
49	chrY:6173766-6173816	H1-hESC	embryonic stem cell:	embryo
50	chrY:6172783-6172833	AoSMC	blood vessel:	n/a

No data

(count:78 , 50 per page) page: 1 2

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AMELY-6	chrY:6111336-6111481	ENSG00000237069.2
2	lnc-AMELY-2	chrY:6276188-6276385	NONHSAT139338
3	lnc-AMELY-2	chrY:6274285-6274964	NONHSAT139338
4	lnc-TSPY2-3	chrY:6320956-6321030	ENSG00000147753
5	lnc-TSPY2-3	chrY:6320956-6321030	ENSG00000147753
6	lnc-AMELY-2	chrY:6279415-6279571	NONHSAT139338
7	lnc-AMELY-4	chrY:6184086-6184282	XLOC_008311
8	lnc-AMELY-6	chrY:6111568-6111670	NONHSAT139331
9	lnc-TSPY2-3	chrY:6318487-6318648	ENSG00000147753
10	lnc-AMELY-1	chrY:6341536-6341671	XLOC_008314
11	lnc-TSPY2-3	chrY:6317509-6317545	XLOC_008281
12	lnc-AMELY-1	chrY:6341536-6341671	XLOC_008314
13	lnc-TSPY2-3	chrY:6325702-6325945	XLOC_008281
14	lnc-AMELY-6	chrY:6111336-6111481	NONHSAT139331
15	lnc-AMELY-4	chrY:6183334-6183506	XLOC_008311
16	lnc-TSPY2-3	chrY:6324014-6324226	XLOC_008281
17	lnc-AMELY-2	chrY:6287806-6287892	XLOC_008313
18	lnc-AMELY-2	chrY:6290369-6292186	XLOC_008313
19	lnc-TSPY2-3	chrY:6318487-6318648	XLOC_008281
20	lnc-AMELY-1	chrY:6341536-6341671	ENSG00000185700
21	lnc-AMELY-11	chrY:6361017-6361112	NONHSAT139346
22	lnc-AMELY-2	chrY:6274286-6274964	XLOC_008313
23	lnc-AMELY-1	chrY:6338814-6338990	XLOC_008314
24	lnc-AMELY-4	chrY:6182796-6182835	XLOC_008311
25	lnc-TSPY2-3	chrY:6321946-6322195	ENSG00000147753
26	lnc-AMELY-2	chrY:6280264-6280412	XLOC_008313
27	lnc-TSPY2-2	chrY:6315014-6315118	ENSG00000237563
28	lnc-TSPY2-3	chrY:6317509-6317545	ENSG00000147753
29	lnc-TSPY2-3	chrY:6325200-6325455	ENSG00000147753
30	lnc-AMELY-1	chrY:6339072-6339261	ENSG00000185700
31	lnc-AMELY-1	chrY:6340854-6341058	XLOC_008314
32	lnc-TSPY2-3	chrY:6320956-6321030	XLOC_008281
33	lnc-AMELY-2	chrY:6276506-6276584	XLOC_008313
34	lnc-AMELY-1	chrY:6339073-6339261	XLOC_008314
35	lnc-TSPY2-3	chrY:6321719-6322195	ENSG00000147753
36	lnc-AMELY-2	chrY:6296281-6296485	XLOC_008313
37	lnc-AMELY-6	chrY:6110487-6110795	ENSG00000237069.2
38	lnc-AMELY-6	chrY:6111595-6111651	ENSG00000237069.2
39	lnc-TSPY2-3	chrY:6317509-6317545	ENSG00000147753
40	lnc-TSPY2-3	chrY:6325702-6325945	XLOC_008281
41	lnc-AMELY-2	chrY:6287806-6287892	XLOC_008313
42	lnc-AMELY-3	chrY:6226725-6226867	XLOC_008312
43	lnc-AMELY-2	chrY:6276506-6276584	NONHSAT139338
44	lnc-TSPY2-3	chrY:6325702-6325947	ENSG00000147753
45	lnc-AMELY-6	chrY:6109809-6109902	NONHSAT139331
46	lnc-TSPY2-3	chrY:6325702-6325947	ENSG00000147753
47	lnc-TSPY2-2	chrY:6315014-6315116	XLOC_008280
48	lnc-TSPY2-3	chrY:6321719-6322195	XLOC_008281
49	lnc-TSPY2-2	chrY:6311475-6311676	XLOC_008280
50	lnc-AMELY-5	chrY:6131875-6131994	ENSG00000234830.2

No data

Variant related genes	Relation type
ENSG00000235895	TF binding region
TTTY21B	TF binding region
ENSG00000250204	TF binding region
ENSG00000251275	TF binding region
TSPY19P	TF binding region
TTTY7	TF binding region
TTTY1B	TF binding region
TSPY17P	TF binding region
TTTY8B	TF binding region
RBMY2GP	TF binding region
FAM197Y9	TF binding region
ENSG00000242879	TF binding region
TSPY11P	TF binding region
LINC00280	TF binding region
TTTY2B	TF binding region
TSPY2	TF binding region
ENSG00000235094	TF binding region
TTTY23B	TF binding region
ENSG00000235895	CpG island
TTTY21B	CpG island
ENSG00000250204	CpG island
ENSG00000251275	CpG island
TSPY19P	CpG island
TTTY7	CpG island
TTTY1B	CpG island
TSPY17P	CpG island
TTTY8B	CpG island
RBMY2GP	CpG island
FAM197Y9	CpG island
ENSG00000242879	CpG island
TSPY11P	CpG island
LINC00280	CpG island
TTTY2B	CpG island
TSPY2	CpG island
ENSG00000235094	CpG island
TTTY23B	CpG island
NR3C1	miRNA target sites
IER3IP1	miRNA target sites
SMCR8	miRNA target sites
STARD7	miRNA target sites
IGF1	miRNA target sites
SNX18	miRNA target sites
MAPRE3	miRNA target sites
IGDCC4	miRNA target sites
MIER3	miRNA target sites
PRUNE2	miRNA target sites
DNMT3A	miRNA target sites

Extended variants
information (count: 187 )
Associated
traits (count: 29 )

Variant overlapped rSNPs/rCNVs (count:187 , 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	rs2558256	chrY:6078126-6078127	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs201446820	chrY:6078134-6078135	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs2767792	chrY:6078156-6078157	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs2558257	chrY:6078238-6078239	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs2558258	chrY:6078461-6078462	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs111969272	chrY:6078471-6078472	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs2558259	chrY:6078540-6078541	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs2433974	chrY:6078616-6078617	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs2433975	chrY:6078652-6078653	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs71302859	chrY:6078691-6078692	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs368169471	chrY:6078844-6078845	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs73612995	chrY:6078994-6078995	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs370394248	chrY:6079114-6079115	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs207480849	chrY:6079143-6079144	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs113028861	chrY:6079604-6079605	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs397833784	chrY:6079967-6079968	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs397833785	chrY:6080041-6080042	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs2558265	chrY:6080042-6080043	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs207480850	chrY:6080828-6080829	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs207480851	chrY:6080960-6080961	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs207480852	chrY:6081025-6081026	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs207480853	chrY:6081256-6081257	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs2558266	chrY:6081368-6081369	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs2558267	chrY:6081371-6081372	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs2767795	chrY:6081426-6081427	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs2767796	chrY:6081483-6081484	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs372535837	chrY:6081496-6081497	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs207480854	chrY:6081571-6081572	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs207480855	chrY:6081704-6081705	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs2558268	chrY:6081803-6081804	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs2433977	chrY:6081834-6081835	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs2433978	chrY:6081884-6081885	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs2433979	chrY:6081930-6081931	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs2558269	chrY:6082075-6082076	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs2558270	chrY:6082084-6082085	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs2767798	chrY:6082128-6082129	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs2790006	chrY:6082283-6082284	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs2792322	chrY:6082289-6082290	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs55752965	chrY:6082610-6082611	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs2099005	chrY:6082905-6082906	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs199817570	chrY:6082913-6082914	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs2081778	chrY:6082930-6082931	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs2081779	chrY:6082933-6082934	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs2558273	chrY:6082979-6082980	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs2356107	chrY:6083033-6083034	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs9785900	chrY:6083116-6083117	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs207480856	chrY:6083148-6083149	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs36057202	chrY:6083481-6083482	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs34062681	chrY:6083607-6083608	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs36072416	chrY:6083618-6083619	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:29)

Disease	PMID	Source
Steroid sulfatase deficiency	22470819	CNVD
Testicular failure	20966427	CNVD
Honadal dysgenesis	22138850	CNVD
severe oligozoospermia and azoospermia	19731213	CNVD
Ewing''s sarcoma	21437220	CNVD
infertility	21210740	CNVD
Klinefelter syndrome	17968468	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
infertility	20668881	CNVD
Klinefelter syndrome	20603808	CNVD
Meiotic abnormalities	17428878	CNVD
Oligozoospermia	20576090	CNVD
Azoospermia	16445861	CNVD
Cryptorchidism	16988323	CNVD
Non-syndromic sensorineural hearing loss	17409464	CNVD
infertile	20603812	CNVD
infertile	22120929	CNVD
infertile	19369647	CNVD
severe oligozoospermia and azoospermia	21887237	CNVD
spermatozoa with elongated heads	17208942	CNVD
Azoospermia	17187159	CNVD
Oligozoospermia	17187159	CNVD
infertile	19440834	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Incontinentia Pigmenti	22033527	CNVD
Intellectual disability	22102821	CNVD
abnormal development	18461090	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrY:6078000-6078400	Enhancers	iPS-20b Cell Line	embryonic stem cell
2	chrY:6078400-6083400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chrY:6083400-6083600	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chrY:6083400-6085200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chrY:6083600-6084000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chrY:6084000-6085000	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chrY:6401600-6403400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
8	chrY:6401800-6402400	ZNF genes & repeats	Fetal Lung	lung
9	chrY:6401800-6402400	ZNF genes & repeats	A549	lung
10	chrY:6401800-6402600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chrY:6401800-6402600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
12	chrY:6401800-6402800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
13	chrY:6401800-6403600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell

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