Variant report

Variant	esv2758903
Chromosome Location	chrY:5955799-6326452
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:650)
CpG islands
(count:1038)
Chromatin interactive
region (count:0)
LncRNA
region (count:68)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:650 , 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	CEBPB	chrY:6058968-6059213	HepG2	liver:	n/a	chrY:6059042-6059053
2	CTCF	chrY:6071944-6072018	GM10266	blood:	n/a	n/a
3	CTCF	chrY:6273760-6273853	GM10266	blood:	n/a	n/a
4	CTCF	chrY:6061648-6061796	Pancreas_OC	pancreas:	n/a	n/a
5	CTCF	chrY:6256818-6256983	ProgFib	skin:	n/a	n/a
6	CTCF	chrY:6103888-6103932	ProgFib	skin:	n/a	n/a
7	CTCF	chrY:6195710-6195887	Pancreas_OC	pancreas:	n/a	n/a
8	CTCF	chrY:5984651-5984730	GM10248	blood:	n/a	n/a
9	CTCF	chrY:6310722-6310782	Medullo	brain:	n/a	n/a
10	CTCF	chrY:6256814-6256979	GM10248	blood:	n/a	n/a
11	CTCF	chrY:6155366-6155455	GM10248	blood:	n/a	n/a
12	CTCF	chrY:5980889-5980906	LNCaP	prostate:	n/a	n/a
13	CTCF	chrY:6078282-6078304	GM10266	blood:	n/a	n/a
14	CTCF	chrY:6174206-6174258	GM10266	blood:	n/a	n/a
15	CTCF	chrY:6210618-6210631	Medullo	brain:	n/a	n/a
16	CTCF	chrY:6025792-6025900	GM20000	blood:	n/a	n/a
17	CTCF	chrY:6275100-6275124	LNCaP	prostate:	n/a	n/a
18	CTCF	chrY:6256792-6256991	GM19239	blood:	n/a	n/a
19	CTCF	chrY:6174260-6174274	GM10266	blood:	n/a	n/a
20	CTCF	chrY:6137487-6137582	LNCaP	prostate:	n/a	n/a
21	CTCF	chrY:6186932-6186942	LNCaP	prostate:	n/a	n/a
22	CTCF	chrY:6230519-6230749	LNCaP	prostate:	n/a	n/a
23	CTCF	chrY:6185267-6185386	GM10248	blood:	n/a	n/a
24	CTCF	chrY:6169340-6169431	GM20000	blood:	n/a	n/a
25	CTCF	chrY:6245870-6245937	Medullo	brain:	n/a	n/a
26	CTCF	chrY:6291133-6291194	LNCaP	prostate:	n/a	n/a
27	CTCF	chrY:6195742-6195743	GM10248	blood:	n/a	n/a
28	CTCF	chrY:6270341-6270394	GM10248	blood:	n/a	n/a
29	CTCF	chrY:6195551-6195687	GM10248	blood:	n/a	n/a
30	CTCF	chrY:6176486-6176640	GM12891	blood:	n/a	n/a
31	CTCF	chrY:6011348-6011459	Medullo	brain:	n/a	n/a
32	CTCF	chrY:6186086-6186168	GM10248	blood:	n/a	n/a
33	CTCF	chrY:6194567-6194662	GM10248	blood:	n/a	n/a
34	CTCF	chrY:6256809-6256966	Pancreas_OC	pancreas:	n/a	n/a
35	CTCF	chrY:6269786-6269862	LNCaP	prostate:	n/a	n/a
36	CTCF	chrY:6082585-6082630	GM10266	blood:	n/a	n/a
37	CTCF	chrY:5978902-5978908	GM20000	blood:	n/a	n/a
38	CTCF	chrY:6091481-6091500	ProgFib	skin:	n/a	n/a
39	CTCF	chrY:6130167-6130252	GM10266	blood:	n/a	n/a
40	CTCF	chrY:5997803-5997914	LNCaP	prostate:	n/a	n/a
41	CTCF	chrY:5968816-5968889	GM20000	blood:	n/a	n/a
42	CTCF	chrY:6144034-6144088	ProgFib	skin:	n/a	n/a
43	CTCF	chrY:6021658-6021726	GM10248	blood:	n/a	n/a
44	CTCF	chrY:6126526-6126558	Medullo	brain:	n/a	n/a
45	CTCF	chrY:6236780-6236806	GM19239	blood:	n/a	n/a
46	CTCF	chrY:6256517-6256657	Medullo	brain:	n/a	n/a
47	CTCF	chrY:6291435-6291500	LNCaP	prostate:	n/a	n/a
48	CTCF	chrY:6105105-6105130	GM10248	blood:	n/a	n/a
49	CTCF	chrY:6178636-6178727	GM20000	blood:	n/a	n/a
50	CTCF	chrY:6324686-6324735	GM10266	blood:	n/a	n/a

(count:1038 , 50 per page) page: 1 2 3 4 5 6 7 ... 21

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chrY:6114404-6114454	GM12878	blood:	n/a
2	chrY:6114404-6114454	GM12878	blood:	n/a
3	chrY:6172783-6172833	Jurkat	blood:	n/a
4	chrY:6263841-6263891	T-47D	breast:	n/a
5	chrY:6131963-6132013	HCF	heart:	n/a
6	chrY:6172428-6172478	BE2_C	brain:	n/a
7	chrY:6173766-6173816	GM12878	blood:	n/a
8	chrY:6312218-6312268	HCPEpiC	choroid plexus:	n/a
9	chrY:6114404-6114454	Hela-S3	cervix:	n/a
10	chrY:6133838-6133888	HNPCEpiC	eye:	n/a
11	chrY:6117321-6117371	HAEpiC	amniotic membrane:	n/a
12	chrY:6114404-6114454	H1-hESC	embryonic stem cell:	embryo
13	chrY:6134650-6134700	IMR90	lung:	fetal
14	chrY:6114255-6114305	IMR90	lung:	fetal
15	chrY:6134650-6134700	HL-60	blood:	n/a
16	chrY:6136711-6136761	K562	blood:	n/a
17	chrY:6114379-6114429	HUVEC	blood vessel:	n/a
18	chrY:6137453-6137503	NHDF-neo	bronchial:	n/a
19	chrY:6173766-6173816	GM12891	blood:	n/a
20	chrY:6263841-6263891	AG09309	skin:	n/a
21	chrY:6117321-6117371	Caco-2	colon:	n/a
22	chrY:6114255-6114305	SKMC	muscle:	n/a
23	chrY:6131963-6132013	GM12892	blood:	n/a
24	chrY:6172783-6172833	AG10803	skin:	n/a
25	chrY:6134650-6134700	NH-A	brain:	n/a
26	chrY:6131963-6132013	BE2_C	brain:	n/a
27	chrY:6113261-6113311	GM12892	blood:	n/a
28	chrY:6263841-6263891	CMK	blood:	n/a
29	chrY:6131007-6131057	HEK293	kidney:	embryo
30	chrY:6173766-6173816	T-47D	breast:	n/a
31	chrY:6173766-6173816	SK-N-SH	brain:	n/a
32	chrY:6136711-6136761	AoSMC	blood vessel:	n/a
33	chrY:6133838-6133888	RPTEC	kidney:	n/a
34	chrY:6263841-6263891	HUVEC	blood vessel:	n/a
35	chrY:6114255-6114305	CMK	blood:	n/a
36	chrY:6131007-6131057	AG04449	skin:	fetal
37	chrY:6117321-6117371	LNCaP	prostate:	n/a
38	chrY:6137453-6137503	MCF10A-Er-Src	breast:	n/a
39	chrY:6263841-6263891	A549	lung:	n/a
40	chrY:6137453-6137503	HEEpiC	esophagus:	n/a
41	chrY:6173766-6173816	U87	brain:	n/a
42	chrY:6114255-6114305	T-47D	breast:	n/a
43	chrY:6131963-6132013	SK-N-MC	brain:	n/a
44	chrY:6312218-6312268	GM06990	blood:	n/a
45	chrY:6136711-6136761	ovcar-3	ovarian:	n/a
46	chrY:6117321-6117371	HMEC	breast:	n/a
47	chrY:6173766-6173816	HMEC	breast:	n/a
48	chrY:6263841-6263891	IMR90	lung:	fetal
49	chrY:6114379-6114429	RPTEC	kidney:	n/a
50	chrY:6173766-6173816	NHDF-neo	bronchial:	n/a

No data

(count:68 , 50 per page) page: 1 2

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TSPY2-3	chrY:6318487-6318648	ENSG00000147753
2	lnc-TSPY2-5	chrY:6026843-6027306	NONHSAT139330
3	lnc-TSPY2-3	chrY:6317509-6317545	XLOC_008281
4	lnc-TSPY2-3	chrY:6325702-6325945	XLOC_008281
5	lnc-TSPY2-2	chrY:6311475-6311676	ENSG00000237563
6	lnc-AMELY-2	chrY:6276188-6276385	NONHSAT139338
7	lnc-TSPY2-3	chrY:6324014-6324226	ENSG00000147753
8	lnc-TSPY2-3	chrY:6324113-6324226	ENSG00000147753
9	lnc-AMELY-2	chrY:6274285-6274964	NONHSAT139338
10	lnc-TSPY2-3	chrY:6325702-6325947	ENSG00000147753
11	lnc-AMELY-2	chrY:6279415-6279571	XLOC_008313
12	lnc-AMELY-4	chrY:6182796-6182835	XLOC_008311
13	lnc-TSPY2-3	chrY:6321719-6322195	ENSG00000147753
14	lnc-AMELY-2	chrY:6287806-6287892	XLOC_008313
15	lnc-TSPY2-2	chrY:6311475-6311676	XLOC_008280
16	lnc-AMELY-6	chrY:6111568-6111670	NONHSAT139331
17	lnc-AMELY-2	chrY:6296281-6296485	NONHSAT139338
18	lnc-TSPY2-3	chrY:6324113-6324226	XLOC_008281
19	lnc-AMELY-2	chrY:6279415-6279571	XLOC_008313
20	lnc-AMELY-2	chrY:6290369-6290446	XLOC_008313
21	lnc-AMELY-2	chrY:6276506-6276584	NONHSAT139338
22	lnc-AMELY-2	chrY:6296281-6296485	XLOC_008313
23	lnc-AMELY-2	chrY:6280264-6280412	XLOC_008313
24	lnc-AMELY-2	chrY:6276188-6276385	XLOC_008313
25	lnc-AMELY-2	chrY:6290369-6292186	XLOC_008313
26	lnc-AMELY-6	chrY:6111336-6111481	NONHSAT139331
27	lnc-AMELY-6	chrY:6111336-6111481	ENSG00000237069.2
28	lnc-TSPY2-3	chrY:6318487-6318648	ENSG00000147753
29	lnc-TSPY2-3	chrY:6321946-6322195	ENSG00000147753
30	lnc-TSPY2-3	chrY:6320956-6321030	XLOC_008281
31	lnc-AMELY-6	chrY:6111595-6111651	ENSG00000237069.2
32	lnc-TSPY2-3	chrY:6320956-6321030	ENSG00000147753
33	lnc-AMELY-2	chrY:6287806-6287892	XLOC_008313
34	lnc-AMELY-2	chrY:6274285-6274964	XLOC_008313
35	lnc-AMELY-2	chrY:6280264-6280412	XLOC_008313
36	lnc-TSPY2-3	chrY:6317509-6317545	ENSG00000147753
37	lnc-AMELY-2	chrY:6287806-6287892	NONHSAT139338
38	lnc-AMELY-2	chrY:6290369-6290446	NONHSAT139338
39	lnc-TSPY2-2	chrY:6315014-6315116	XLOC_008280
40	lnc-AMELY-2	chrY:6279415-6279571	NONHSAT139338
41	lnc-AMELY-5	chrY:6129985-6130070	ENSG00000234830.2
42	lnc-AMELY-2	chrY:6276188-6276385	XLOC_008313
43	lnc-AMELY-3	chrY:6225260-6225478	XLOC_008312
44	lnc-TSPY2-2	chrY:6315014-6315118	ENSG00000237563
45	lnc-AMELY-2	chrY:6280264-6280412	NONHSAT139338
46	lnc-TSPY2-3	chrY:6324014-6324226	XLOC_008281
47	lnc-TSPY2-3	chrY:6325200-6325455	ENSG00000147753
48	lnc-AMELY-5	chrY:6124308-6126433	ENSG00000234830.2
49	lnc-TSPY2-3	chrY:6321719-6322195	XLOC_008281
50	lnc-TSPY2-3	chrY:6318487-6318648	XLOC_008281

No data

Variant related genes	Relation type
RBMY2GP	TF binding region
DLGAP5P1	TF binding region
ENSG00000251275	TF binding region
TTTY21B	TF binding region
TTTY7	TF binding region
FAM197Y9	TF binding region
TTTY2B	TF binding region
TTTY23B	TF binding region
ENSG00000242879	TF binding region
TSPY2	TF binding region
ENSG00000250204	TF binding region
TSPY19P	TF binding region
TSPY11P	TF binding region
LINC00280	TF binding region
ENSG00000235094	TF binding region
TTTY1B	TF binding region
RBMY2GP	CpG island
DLGAP5P1	CpG island
ENSG00000251275	CpG island
TTTY21B	CpG island
TTTY7	CpG island
FAM197Y9	CpG island
TTTY2B	CpG island
TTTY23B	CpG island
ENSG00000242879	CpG island
TSPY2	CpG island
ENSG00000250204	CpG island
TSPY19P	CpG island
TSPY11P	CpG island
LINC00280	CpG island
ENSG00000235094	CpG island
TTTY1B	CpG island
SMCR8	miRNA target sites
NR3C1	miRNA target sites
IGDCC4	miRNA target sites
IER3IP1	miRNA target sites
PRUNE2	miRNA target sites
MAPRE3	miRNA target sites
MIER3	miRNA target sites
IGF1	miRNA target sites

Extended variants
information (count: 148 )
Associated
traits (count: 29 )

Variant overlapped rSNPs/rCNVs (count:148 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs575127806	chrY:5998156-5998157	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs370749766	chrY:5998261-5998262	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs373023231	chrY:5998491-5998492	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs34014055	chrY:5998806-5998807	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs35361412	chrY:5998809-5998810	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs4027906	chrY:5998972-5998973	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs3951034	chrY:5999003-5999004	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs370506133	chrY:5999035-5999036	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs2767882	chrY:5999079-5999080	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs2767883	chrY:5999080-5999081	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs2767884	chrY:5999139-5999140	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs374058610	chrY:5999271-5999272	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs4027890	chrY:5999306-5999307	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs73612993	chrY:5999355-5999356	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs73612994	chrY:5999533-5999534	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs207480781	chrY:5999679-5999680	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs207480782	chrY:5999685-5999686	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs207480783	chrY:5999833-5999834	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs374449875	chrY:5999836-5999837	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs9786527	chrY:5999859-5999860	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs207480784	chrY:5999869-5999870	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs36062389	chrY:5999942-5999943	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs111313139	chrY:6000030-6000031	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs367547420	chrY:6000146-6000147	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs568146592	chrY:6000185-6000186	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs7067483	chrY:6000464-6000465	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs4617339	chrY:6000520-6000521	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs207480786	chrY:6000625-6000626	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs207480787	chrY:6000713-6000714	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs207480788	chrY:6000754-6000755	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs76303663	chrY:6004228-6004229	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs207480795	chrY:6004247-6004248	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs207480798	chrY:6006838-6006839	Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs112368780	chrY:6007087-6007088	Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs113118964	chrY:6007127-6007128	Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs112379147	chrY:6007257-6007258	Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs13304013	chrY:6007290-6007291	Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs371113284	chrY:6007291-6007292	Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs34917221	chrY:6007305-6007306	Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs34839072	chrY:6007384-6007385	Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs200931641	chrY:6025874-6025875	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs207480803	chrY:6026921-6026922	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
43	rs207480804	chrY:6027201-6027202	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
44	rs113267606	chrY:6027274-6027275	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
45	rs4028014	chrY:6073132-6073133	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs4028015	chrY:6073168-6073169	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs2558229	chrY:6073227-6073228	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs4028017	chrY:6073287-6073288	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs2558230	chrY:6073341-6073342	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs4028019	chrY:6073345-6073346	Enhancers	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:5998000-5999000	Enhancers	iPS-20b Cell Line	embryonic stem cell
2	chrY:5999000-5999400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chrY:5999400-6000800	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chrY:5999600-6000200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chrY:6004000-6004400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chrY:6006800-6007400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chrY:6073000-6073400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chrY:6078000-6078400	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chrY:6078400-6083400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chrY:6083400-6083600	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chrY:6083400-6085200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chrY:6083600-6084000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chrY:6084000-6085000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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