Variant report

Variant	esv3409548
Chromosome Location	chrY:16169870-17053457
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	ARID3A	chrY:16740017-16740510	HepG2	liver:	n/a	n/a
2	ARID3A	chrY:16874744-16875075	HepG2	liver:	n/a	n/a
3	ARID3A	chrY:16452621-16452866	HepG2	liver:	n/a	n/a
4	ARID3A	chrY:16456759-16457216	HepG2	liver:	n/a	n/a
5	ARID3A	chrY:16636195-16636567	HepG2	liver:	n/a	n/a
6	ARID3A	chrY:16746925-16747352	HepG2	liver:	n/a	n/a
7	ARID3A	chrY:16637349-16637562	HepG2	liver:	n/a	n/a
8	BCL3	chrY:16452535-16453093	A549	lung:	n/a	n/a
9	BCL3	chrY:16452590-16453112	A549	lung:	n/a	n/a
10	BHLHE40	chrY:16930420-16930717	HepG2	liver:	n/a	n/a
11	BHLHE40	chrY:16740192-16740477	HepG2	liver:	n/a	n/a
12	CEBPB	chrY:16962694-16962903	HepG2	liver:	n/a	chrY:16962800-16962811 chrY:16962824-16962835 chrY:16962776-16962787
13	CEBPB	chrY:16875570-16875697	HepG2	liver:	n/a	chrY:16875638-16875649
14	CEBPB	chrY:16875508-16876477	HepG2	liver:	n/a	chrY:16875638-16875649
15	CEBPB	chrY:16333950-16334209	HepG2	liver:	n/a	n/a
16	CEBPB	chrY:16962578-16962961	A549	lung:	n/a	chrY:16962800-16962811 chrY:16962824-16962835 chrY:16962776-16962787
17	CEBPB	chrY:16740105-16740477	HepG2	liver:	n/a	chrY:16740278-16740289
18	CEBPB	chrY:16591209-16591503	HepG2	liver:	n/a	chrY:16591332-16591343
19	CEBPB	chrY:16973035-16973306	HepG2	liver:	n/a	n/a
20	CEBPB	chrY:17020597-17020723	A549	lung:	n/a	n/a
21	CEBPB	chrY:16817174-16817348	A549	lung:	n/a	n/a
22	CEBPB	chrY:16642314-16642645	A549	lung:	n/a	chrY:16642498-16642509 chrY:16642475-16642486
23	CEBPB	chrY:16740169-16740386	HepG2	liver:	n/a	chrY:16740278-16740289
24	CEBPB	chrY:16642300-16642633	HepG2	liver:	n/a	chrY:16642498-16642509 chrY:16642475-16642486
25	CEBPB	chrY:16594136-16594437	HepG2	liver:	n/a	chrY:16594278-16594289
26	CEBPB	chrY:16597318-16597545	HepG2	liver:	n/a	chrY:16597418-16597429
27	CEBPB	chrY:16962622-16962983	A549	lung:	n/a	chrY:16962800-16962811 chrY:16962824-16962835 chrY:16962776-16962787
28	CEBPB	chrY:16836849-16837101	HepG2	liver:	n/a	chrY:16836977-16836988
29	CEBPB	chrY:16962658-16962903	HepG2	liver:	n/a	chrY:16962800-16962811 chrY:16962824-16962835 chrY:16962776-16962787
30	CEBPB	chrY:16962655-16962931	A549	lung:	n/a	chrY:16962800-16962811 chrY:16962824-16962835 chrY:16962776-16962787
31	CEBPB	chrY:16535562-16535897	HepG2	liver:	n/a	n/a
32	CEBPB	chrY:16623109-16623469	HepG2	liver:	n/a	chrY:16623282-16623293
33	CEBPB	chrY:16962606-16963005	HepG2	liver:	n/a	chrY:16962800-16962811 chrY:16962824-16962835 chrY:16962776-16962787
34	CEBPD	chrY:16962642-16962877	HepG2	liver:	n/a	n/a
35	CHD2	chrY:16636326-16636849	HepG2	liver:	n/a	n/a
36	CREB1	chrY:16740117-16740570	HepG2	liver:	n/a	n/a
37	CTCF	chrY:16838837-16838896	GM20000	blood:	n/a	n/a
38	CTCF	chrY:16990934-16990996	GM20000	blood:	n/a	n/a
39	CTCF	chrY:16730400-16730550	NHDF-neo	bronchial:	n/a	n/a
40	CTCF	chrY:16729620-16729770	AG10803	skin:	n/a	n/a
41	CTCF	chrY:16889617-16889633	GM10266	blood:	n/a	n/a
42	CTCF	chrY:16730480-16730630	AG10803	skin:	n/a	n/a
43	CTCF	chrY:16905539-16905628	GM12891	blood:	n/a	n/a
44	CTCF	chrY:16730493-16730659	HUVEC	blood vessel:	n/a	n/a
45	CTCF	chrY:16729680-16729830	GM12871	blood:	n/a	n/a
46	CTCF	chrY:16219698-16219719	GM10266	blood:	n/a	n/a
47	CTCF	chrY:16730503-16730664	ProgFib	skin:	n/a	n/a
48	CTCF	chrY:16508328-16508380	Pancreas_OC	pancreas:	n/a	n/a
49	CTCF	chrY:16807880-16808030	HPAF	blood vessel:	n/a	n/a
50	CTCF	chrY:16637380-16637530	HPF	lung:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chrY:16939383-16939433	T-47D	breast:	n/a
2	chrY:16942154-16942204	HEK293	kidney:	embryo
3	chrY:16939383-16939433	T-47D	breast:	n/a
4	chrY:16942154-16942204	HEK293	kidney:	embryo
5	chrY:16634255-16634305	H1-hESC	embryonic stem cell:	embryo
6	chrY:16636258-16636308	HNPCEpiC	eye:	n/a
7	chrY:16634382-16634432	NH-A	brain:	n/a
8	chrY:16733930-16733980	HepG2	liver:	n/a
9	chrY:16632438-16632488	SAEC	small airway:	n/a
10	chrY:16635501-16635551	H1-hESC	embryonic stem cell:	embryo
11	chrY:16634373-16634423	LNCaP	prostate:	n/a
12	chrY:16632438-16632488	AG04450	lung:	fetal
13	chrY:16636990-16637040	AG09309	skin:	n/a
14	chrY:16634126-16634176	NHBE	bronchial:	n/a
15	chrY:16637061-16637111	HCT-116	colon:	n/a
16	chrY:16942232-16942282	NB4	blood:	n/a
17	chrY:16636697-16636747	HL-60	blood:	n/a
18	chrY:16632438-16632488	MCF-7	breast:	n/a
19	chrY:16635745-16635795	GM06990	blood:	n/a
20	chrY:16939383-16939433	GM12891	blood:	n/a
21	chrY:16634126-16634176	U87	brain:	n/a
22	chrY:16635745-16635795	HPAEpiC	pulmonary alveolar:	n/a
23	chrY:16634594-16634644	MCF10A-Er-Src	breast:	n/a
24	chrY:16924422-16924472	HepG2	liver:	n/a
25	chrY:16635501-16635551	HEEpiC	esophagus:	n/a
26	chrY:16942154-16942204	RPTEC	kidney:	n/a
27	chrY:16945913-16945963	MCF10A-Er-Src	breast:	n/a
28	chrY:16945913-16945963	HMEC	breast:	n/a
29	chrY:16942232-16942282	HL-60	blood:	n/a
30	chrY:16635745-16635795	AoSMC	blood vessel:	n/a
31	chrY:16635501-16635551	A549	lung:	n/a
32	chrY:16637142-16637192	ProgFib	skin:	n/a
33	chrY:16635501-16635551	AG09319	gingival:	n/a
34	chrY:16942154-16942204	HIPEpiC	eye:	n/a
35	chrY:16637142-16637192	HPAEpiC	pulmonary alveolar:	n/a
36	chrY:16733442-16733492	AG04450	lung:	fetal
37	chrY:16942154-16942204	AG04450	lung:	fetal
38	chrY:16636258-16636308	HRCEpiC	kidney:	n/a
39	chrY:16635745-16635795	SK-N-SH_RA	brain:	n/a
40	chrY:16636984-16637034	BJ	skin:	n/a
41	chrY:16636697-16636747	HIPEpiC	eye:	n/a
42	chrY:16634027-16634077	AoSMC	blood vessel:	n/a
43	chrY:16634255-16634305	MCF10A-Er-Src	breast:	n/a
44	chrY:16634126-16634176	PFSK-1	brain:	n/a
45	chrY:16637142-16637192	K562	blood:	n/a
46	chrY:16632438-16632488	SKMC	muscle:	n/a
47	chrY:16939383-16939433	HIPEpiC	eye:	n/a
48	chrY:16945913-16945963	HL-60	blood:	n/a
49	chrY:16945913-16945963	AG10803	skin:	n/a
50	chrY:16635745-16635795	Caco-2	colon:	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VCY1B-2	chrY:16905522-16905867	ENSG00000228787.1
2	lnc-VCY1B-2	chrY:16913156-16913224	ENSG00000228787.1
3	lnc-VCY1B-1	chrY:16388092-16388491	XLOC_008324
4	lnc-VCY1B-1	chrY:16389230-16389369	XLOC_008324
5	lnc-VCY1B-2	chrY:16915885-16915913	ENSG00000228787.1
6	lnc-VCY1B-2	chrY:16910502-16910589	ENSG00000228787.1

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	NLGN4Y	hsa-miR-124-3p	chrY:16955740-16955746

Variant related genes	Relation type
NLGN4Y	TF binding region
ENSG00000224518	TF binding region
PNPLA4P1	TF binding region
MED13P1	TF binding region
ENSG00000266220	TF binding region
NLGN4Y-AS1	TF binding region
AGKP1	TF binding region
ENSG00000223517	TF binding region
NLGN4Y	CpG island
ENSG00000224518	CpG island
PNPLA4P1	CpG island
MED13P1	CpG island
ENSG00000266220	CpG island
NLGN4Y-AS1	CpG island
AGKP1	CpG island
ENSG00000223517	CpG island

Extended variants
information (count: 1526 )
Associated
traits (count: 52 )

Variant overlapped rSNPs/rCNVs (count:1526 , 50 per page) page: 1 2 3 4 5 6 7 ... 31

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs371048738	chrY:16172534-16172535	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs9786133	chrY:16172915-16172916	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs375294106	chrY:16211449-16211450	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs9785796	chrY:16230262-16230263	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs370468863	chrY:16230475-16230476	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs373623136	chrY:16237195-16237196	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs375686213	chrY:16237221-16237222	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs539444727	chrY:16237478-16237479	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs374278314	chrY:16238303-16238304	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs368446737	chrY:16238956-16238957	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs368372500	chrY:16239037-16239038	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs368029920	chrY:16239038-16239039	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs372424117	chrY:16239039-16239040	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs386828808	chrY:16239077-16239078	Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs199635791	chrY:16249652-16249653	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs539944108	chrY:16250280-16250281	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs556336063	chrY:16250619-16250620	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs112322234	chrY:16250624-16250625	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs567910035	chrY:16250625-16250626	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs35742917	chrY:16250659-16250660	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs374544542	chrY:16251340-16251341	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs16980586	chrY:16251357-16251358	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs535898791	chrY:16251671-16251672	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs372331309	chrY:16252528-16252529	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs36047418	chrY:16252668-16252669	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs112655306	chrY:16252670-16252671	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs370795738	chrY:16253005-16253006	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs16980588	chrY:16253694-16253695	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs377282279	chrY:16254005-16254006	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs374456165	chrY:16254006-16254007	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs368572161	chrY:16254560-16254561	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs201385428	chrY:16255201-16255202	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs371844732	chrY:16256048-16256049	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs368854811	chrY:16256100-16256101	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs545894348	chrY:16256397-16256398	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs376976025	chrY:16257054-16257055	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs372447857	chrY:16257600-16257601	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs112038699	chrY:16257654-16257655	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs368444307	chrY:16257835-16257836	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs531304031	chrY:16258006-16258007	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs112789295	chrY:16258090-16258091	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs35623489	chrY:16258314-16258315	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs377380776	chrY:16258805-16258806	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs370214135	chrY:16268345-16268346	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs367663050	chrY:16270909-16270910	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs13305700	chrY:16271151-16271152	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs545728840	chrY:16271260-16271261	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs13304550	chrY:16271262-16271263	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs555921727	chrY:16271515-16271516	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs374283648	chrY:16271535-16271536	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:52)

Disease	PMID	Source
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
Breast cancer	21045282	CNVD
infertility	21340528	CNVD
Klinefelter syndrome	16612480	CNVD
infertile	16612480	CNVD
Infertility	16469004	CNVD
Recurrent pregnancy loss	20943704	CNVD
infertile	16469004	CNVD
infertility	18832950	CNVD
Maturation arrest	22820855	CNVD
Azoospermia	16709604	CNVD
Astheno-teratozoospermia syndrome	22371775	CNVD
Asthenozoospermia	22371775	CNVD
Azoospermia	22371775	CNVD
Oligoasthenoteratozoospermia	22371775	CNVD
Oligoasthenozoospermia	22371775	CNVD
Oligoteratozoospermia	22371775	CNVD
Teratozoospermia	22371775	CNVD
infertile	17554051	CNVD
Klinefelter syndrome	20805717	CNVD
subfertile	22371775	CNVD
infertile	19966830	CNVD
Azoospermia	20823911	CNVD
Non-syndromic sensorineural hearing loss	18200580	CNVD
infertile oligozoospermic	17712493	CNVD
Hereditary coagulopathy	21993689	CNVD
Honadal dysgenesis	21048976	CNVD
Melanoma	22183965	CNVD
Cancer	22183965	CNVD

Chromatin state (count:969 , 50 per page) page: 1 2 3 4 5 6 7 ... 20

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrY:16172400-16173200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chrY:16211400-16212200	Enhancers	Dnd41	blood
3	chrY:16219600-16219800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chrY:16230200-16230800	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chrY:16237000-16238600	Enhancers	Fetal Heart	heart
6	chrY:16237200-16237600	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chrY:16238400-16239000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chrY:16239000-16239200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chrY:16249000-16251200	Weak transcription	Fetal Heart	heart
10	chrY:16249000-16251600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chrY:16251000-16251800	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chrY:16251200-16252600	Enhancers	Fetal Heart	heart
13	chrY:16251400-16251800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chrY:16251600-16251800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chrY:16251600-16252200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chrY:16251800-16252200	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chrY:16251800-16252800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chrY:16252200-16255800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chrY:16252400-16254600	Enhancers	Dnd41	blood
20	chrY:16252600-16255600	Weak transcription	Fetal Heart	heart
21	chrY:16252800-16253600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chrY:16253800-16254000	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chrY:16254400-16255800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chrY:16254600-16255800	Weak transcription	Dnd41	blood
25	chrY:16255600-16256200	Enhancers	Fetal Heart	heart
26	chrY:16255800-16256200	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chrY:16255800-16256600	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chrY:16255800-16259600	Enhancers	Dnd41	blood
29	chrY:16256600-16257800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chrY:16257800-16258000	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chrY:16268000-16268800	Enhancers	Stomach Mucosa	stomach
32	chrY:16270600-16271800	Enhancers	Dnd41	blood
33	chrY:16294600-16295000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chrY:16306400-16306600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chrY:16318200-16318600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chrY:16333800-16334600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chrY:16334600-16335400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chrY:16335400-16335600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chrY:16344800-16345000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
40	chrY:16358600-16359600	Enhancers	Brain Hippocampus Middle	brain
41	chrY:16359000-16359200	Enhancers	Dnd41	blood
42	chrY:16359200-16360200	Weak transcription	Dnd41	blood
43	chrY:16360200-16361600	Enhancers	Dnd41	blood
44	chrY:16361600-16366600	Weak transcription	Dnd41	blood
45	chrY:16366600-16367400	Enhancers	Dnd41	blood
46	chrY:16367000-16370000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chrY:16367200-16369200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chrY:16367200-16369200	Enhancers	Thymus	Thymus
49	chrY:16367400-16368400	Flanking Active TSS	Dnd41	blood
50	chrY:16367600-16368200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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