Variant report

Variant	esv3384643
Chromosome Location	chrX:55919980-55939813
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:325)
CpG islands
(count:366)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:325 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BATF	chrX:55934725-55935034	GM12878	blood:	n/a	n/a
2	BCLAF1	chrX:55934376-55934737	GM12878	blood:	n/a	n/a
3	BCLAF1	chrX:55934329-55934804	GM12878	blood:	n/a	n/a
4	BHLHE40	chrX:55934433-55934869	GM12878	blood:	n/a	n/a
5	CHD2	chrX:55929696-55929775	K562	blood:	n/a	n/a
6	CHD2	chrX:55935161-55935416	GM12878	blood:	n/a	n/a
7	CHD2	chrX:55934438-55934871	GM12878	blood:	n/a	n/a
8	CTCF	chrX:55934471-55934723	Gliobla	brain:	n/a	n/a
9	CTCF	chrX:55934424-55934750	GM19238	blood:	n/a	n/a
10	CTCF	chrX:55934520-55934670	HCM	heart:	n/a	n/a
11	CTCF	chrX:55934480-55934630	GM12869	blood:	n/a	n/a
12	CTCF	chrX:55934540-55934690	GM12870	blood:	n/a	n/a
13	CTCF	chrX:55934560-55934710	AG04449	skin:	n/a	n/a
14	CTCF	chrX:55925164-55925244	GM10248	blood:	n/a	n/a
15	CTCF	chrX:55934480-55934630	AG10803	skin:	n/a	n/a
16	CTCF	chrX:55934440-55934590	MCF-7	breast:	n/a	n/a
17	CTCF	chrX:55934580-55934730	HEEpiC	esophagus:	n/a	n/a
18	CTCF	chrX:55934540-55934690	RPTEC	kidney:	n/a	n/a
19	CTCF	chrX:55934520-55934670	GM06990	blood:	n/a	n/a
20	CTCF	chrX:55934500-55934650	SK-N-SH_RA	brain:	n/a	n/a
21	CTCF	chrX:55934500-55934650	K562	blood:	n/a	n/a
22	CTCF	chrX:55934400-55934550	NHEK	skin:	n/a	n/a
23	CTCF	chrX:55934346-55934883	MCF-7	breast:	n/a	n/a
24	CTCF	chrX:55934460-55934610	GM12870	blood:	n/a	n/a
25	CTCF	chrX:55934500-55934650	Caco-2	colon:	n/a	n/a
26	CTCF	chrX:55934520-55934670	GM12865	blood:	n/a	n/a
27	CTCF	chrX:55934500-55934650	GM12866	blood:	n/a	n/a
28	CTCF	chrX:55934523-55934747	ProgFib	skin:	n/a	n/a
29	CTCF	chrX:55934540-55934690	HMF	breast:	n/a	n/a
30	CTCF	chrX:55934560-55934710	HCPEpiC	choroid plexus:	n/a	n/a
31	CTCF	chrX:55934456-55934691	K562	blood:	n/a	n/a
32	CTCF	chrX:55934520-55934670	GM12874	blood:	n/a	n/a
33	CTCF	chrX:55934566-55934683	A549	lung:	n/a	n/a
34	CTCF	chrX:55934500-55934650	HA-sp	spinal cord:	n/a	n/a
35	CTCF	chrX:55934620-55934770	GM12801	blood:	n/a	n/a
36	CTCF	chrX:55934560-55934710	GM12865	blood:	n/a	n/a
37	CTCF	chrX:55934528-55934720	NHEK	skin:	n/a	n/a
38	CTCF	chrX:55935260-55935410	SAEC	small airway:	n/a	n/a
39	CTCF	chrX:55934520-55934670	NHEK	skin:	n/a	n/a
40	CTCF	chrX:55934540-55934690	GM12868	blood:	n/a	n/a
41	CTCF	chrX:55934540-55934690	GM12873	blood:	n/a	n/a
42	CTCF	chrX:55934469-55934699	Kidney_OC	kidney:	n/a	n/a
43	CTCF	chrX:55924135-55924176	GM10248	blood:	n/a	n/a
44	CTCF	chrX:55934500-55934650	AG09309	skin:	n/a	n/a
45	CTCF	chrX:55934513-55934657	SK-N-SH_RA	brain:	n/a	n/a
46	CTCF	chrX:55934468-55934742	GM12878	blood:	n/a	n/a
47	CTCF	chrX:55934560-55934710	HPAF	blood vessel:	n/a	n/a
48	CTCF	chrX:55934332-55934761	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chrX:55935200-55935350	GM12875	blood:	n/a	n/a
50	CTCF	chrX:55934520-55934670	GM12878	blood:	n/a	n/a

(count:366 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chrX:55934800-55934850	HCT-116	colon:	n/a
2	chrX:55934745-55934795	SK-N-MC	brain:	n/a
3	chrX:55934874-55934924	Hela-S3	cervix:	n/a
4	chrX:55934745-55934795	HCF	heart:	n/a
5	chrX:55934745-55934795	H1-hESC	embryonic stem cell:	embryo
6	chrX:55935143-55935193	Hela-S3	cervix:	n/a
7	chrX:55934670-55934720	LNCaP	prostate:	n/a
8	chrX:55934800-55934850	A549	lung:	n/a
9	chrX:55935071-55935121	AG10803	skin:	n/a
10	chrX:55934800-55934850	PFSK-1	brain:	n/a
11	chrX:55935143-55935193	HRPEpiC	eye:	n/a
12	chrX:55934670-55934720	HCT-116	colon:	n/a
13	chrX:55934800-55934850	IMR90	lung:	fetal
14	chrX:55935071-55935121	Jurkat	blood:	n/a
15	chrX:55934874-55934924	SK-N-SH	brain:	n/a
16	chrX:55934670-55934720	HIPEpiC	eye:	n/a
17	chrX:55934800-55934850	Hela-S3	cervix:	n/a
18	chrX:55934874-55934924	HEEpiC	esophagus:	n/a
19	chrX:55934874-55934924	LNCaP	prostate:	n/a
20	chrX:55934670-55934720	GM12892	blood:	n/a
21	chrX:55935071-55935121	SAEC	small airway:	n/a
22	chrX:55935071-55935121	NH-A	brain:	n/a
23	chrX:55934874-55934924	GM19239	blood:	n/a
24	chrX:55935143-55935193	AG04450	lung:	fetal
25	chrX:55935071-55935121	BJ	skin:	n/a
26	chrX:55934745-55934795	ECC-1	luminal epithelium:	n/a
27	chrX:55935071-55935121	SKMC	muscle:	n/a
28	chrX:55934874-55934924	NHDF-neo	bronchial:	n/a
29	chrX:55934670-55934720	AG10803	skin:	n/a
30	chrX:55934874-55934924	Caco-2	colon:	n/a
31	chrX:55935071-55935121	GM12878	blood:	n/a
32	chrX:55934874-55934924	MCF10A-Er-Src	breast:	n/a
33	chrX:55934670-55934720	ECC-1	luminal epithelium:	n/a
34	chrX:55934874-55934924	HIPEpiC	eye:	n/a
35	chrX:55935071-55935121	NHDF-neo	bronchial:	n/a
36	chrX:55934800-55934850	HL-60	blood:	n/a
37	chrX:55934800-55934850	AG09309	skin:	n/a
38	chrX:55934800-55934850	ovcar-3	ovarian:	n/a
39	chrX:55934745-55934795	HRCEpiC	kidney:	n/a
40	chrX:55935143-55935193	HAEpiC	amniotic membrane:	n/a
41	chrX:55934874-55934924	BJ	skin:	n/a
42	chrX:55934670-55934720	GM12878	blood:	n/a
43	chrX:55935143-55935193	BJ	skin:	n/a
44	chrX:55934745-55934795	HepG2	liver:	n/a
45	chrX:55934670-55934720	K562	blood:	n/a
46	chrX:55934800-55934850	ECC-1	luminal epithelium:	n/a
47	chrX:55934800-55934850	HRCEpiC	kidney:	n/a
48	chrX:55934670-55934720	GM12891	blood:	n/a
49	chrX:55934745-55934795	NHDF-neo	bronchial:	n/a
50	chrX:55934800-55934850	SK-N-SH	brain:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:55933333..55936298-chrX:55937744..55939331,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL353698.1-1	chrX:55937880-55938503	NONHSAT137261
2	lnc-AL353698.1-2	chrX:55934556-55935233	ENSG00000227486.1

No data

Variant related genes	Relation type
ENSG00000252961	TF binding region
ENSG00000227486	TF binding region
ENSG00000252961	CpG island
ENSG00000227486	CpG island
ENSG00000227486	chromatin interactions

Extended variants
information (count: 109 )
Associated
traits (count: 41 )

Variant overlapped rSNPs/rCNVs (count:109 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs374682562	chrX:55929729-55929730	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs138081269	chrX:55929737-55929738	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs371591510	chrX:55930222-55930223	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs374689381	chrX:55930226-55930227	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs190817054	chrX:55930288-55930289	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs373678768	chrX:55930353-55930354	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs368539792	chrX:55930384-55930385	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs554248954	chrX:55930403-55930404	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs183416308	chrX:55930428-55930429	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
10	rs188847122	chrX:55930583-55930584	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
11	rs191731032	chrX:55930745-55930746	ZNF genes & repeats	TF binding region	2 gene(s)	Overlapped CNVs	n/a
12	rs5960112	chrX:55930768-55930769	ZNF genes & repeats	TF binding region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs371920867	chrX:55930832-55930833	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
14	rs183434083	chrX:55930836-55930837	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
15	rs188094107	chrX:55930896-55930897	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
16	rs191901894	chrX:55930914-55930915	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs558796111	chrX:55930922-55930923	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
18	rs183762364	chrX:55931021-55931022	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
19	rs138115030	chrX:55931076-55931077	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
20	rs186902364	chrX:55931084-55931085	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
21	rs192470590	chrX:55931418-55931419	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
22	rs185545683	chrX:55931456-55931457	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs7064903	chrX:55931501-55931502	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
24	rs34365561	chrX:55931617-55931618	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
25	rs372639162	chrX:55931710-55931711	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
26	rs57673580	chrX:55931732-55931733	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
27	rs190470485	chrX:55931905-55931906	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs181636840	chrX:55931982-55931983	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
29	rs142097920	chrX:55931983-55931984	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs185336248	chrX:55931985-55931986	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs188535169	chrX:55932111-55932112	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
32	rs73622954	chrX:55932181-55932182	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs139588164	chrX:55932339-55932340	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs200663770	chrX:55932365-55932366	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs181295972	chrX:55932398-55932399	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs375954370	chrX:55932538-55932539	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
37	rs12834583	chrX:55932569-55932570	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
38	rs73622955	chrX:55932575-55932576	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
39	rs73622956	chrX:55932738-55932739	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
40	rs185030510	chrX:55932860-55932861	Weak transcription Flanking Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
41	rs188021142	chrX:55932947-55932948	Weak transcription Flanking Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
42	rs369724367	chrX:55933011-55933012	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs60270467	chrX:55933162-55933163	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs180934272	chrX:55933206-55933207	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs535490239	chrX:55933308-55933309	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs139936606	chrX:55933471-55933472	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs149853978	chrX:55933574-55933575	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs187193682	chrX:55933575-55933576	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs145795559	chrX:55933612-55933613	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs191985124	chrX:55933846-55933847	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:41)

Disease	PMID	Source
Cancer	21637783	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Cancer	16751803	CNVD
Intellectual disability	23615299	CNVD
Neuroblastoma	18923191	CNVD
Burkitt''s lymphoma	20823134	CNVD
Astrocytoma	17387387	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Metanephric adenoma	20802469	CNVD
Medulloblastoma	21979893	CNVD
Schizophrenia	23904455	CNVD
Olfactory neuroblastoma	18408657	CNVD
infertile	22614455	CNVD
Acute myeloid leukemia	20729466	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Glioblastoma multiforme	22286061	CNVD
Acute myeloid leukemia	21251322	CNVD
Cancer	20581869	CNVD
Multiple myeloma	20724749	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
small cell lung cancer	20016488	CNVD
Prostate cancer	18632612	CNVD
Lung cancer	18438408	CNVD
Cancer	20164919	CNVD
Premature ovarian failure	20952765	CNVD
Thyroid cancer	19087340	CNVD
lymphocytic leukemia	21291569	CNVD
Cervical cancer	21062161	CNVD
Follicular lymphoma	20505157	CNVD
primary effusion lymphomas	17116491	CNVD
Testicular germ cell tumor	18059402	CNVD
Testicular cancer	18059402	CNVD
Seminomas	18059402	CNVD
Breast cancer	21785460	CNVD
Ovarian cancer	19835627	CNVD
Mental retardation	21735175	CNVD

Chromatin state (count:272 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:55930200-55932200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chrX:55932200-55933600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chrX:55932600-55932800	Enhancers	GM12878-XiMat	blood
4	chrX:55932800-55933000	Flanking Active TSS	GM12878-XiMat	blood
5	chrX:55933000-55933600	Active TSS	GM12878-XiMat	blood
6	chrX:55933600-55933800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
7	chrX:55933600-55933800	Enhancers	Placenta Amnion	Placenta Amnion
8	chrX:55933600-55933800	Enhancers	GM12878-XiMat	blood
9	chrX:55933600-55934400	Enhancers	Primary B cells from peripheral blood	blood
10	chrX:55933600-55936400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
11	chrX:55933600-55939000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chrX:55933800-55934000	Enhancers	H1 Cell Line	embryonic stem cell
13	chrX:55933800-55934000	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chrX:55933800-55934000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chrX:55933800-55934000	Flanking Active TSS	GM12878-XiMat	blood
16	chrX:55933800-55934200	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chrX:55933800-55934200	Enhancers	Fetal Intestine Small	intestine
18	chrX:55933800-55936200	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chrX:55934000-55934200	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chrX:55934000-55934200	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chrX:55934000-55934200	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chrX:55934000-55934200	Enhancers	Fetal Intestine Large	intestine
23	chrX:55934000-55934200	Enhancers	Fetal Thymus	thymus
24	chrX:55934000-55934400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
25	chrX:55934000-55934400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chrX:55934000-55934400	Enhancers	Brain Cingulate Gyrus	brain
27	chrX:55934000-55934400	Enhancers	Brain Inferior Temporal Lobe	brain
28	chrX:55934000-55936000	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chrX:55934000-55936000	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chrX:55934000-55936000	Active TSS	Rectal Smooth Muscle	rectum
31	chrX:55934000-55938800	Active TSS	GM12878-XiMat	blood
32	chrX:55934200-55934400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chrX:55934200-55934400	Enhancers	Primary T cells fromperipheralblood	blood
34	chrX:55934200-55934400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chrX:55934200-55934400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chrX:55934200-55934400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
37	chrX:55934200-55934400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chrX:55934200-55934400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chrX:55934200-55934400	Enhancers	Aorta	Aorta
40	chrX:55934200-55934400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chrX:55934200-55934400	Flanking Active TSS	Fetal Intestine Large	intestine
42	chrX:55934200-55934400	Flanking Active TSS	Fetal Intestine Small	intestine
43	chrX:55934200-55934400	Flanking Active TSS	Fetal Kidney	kidney
44	chrX:55934200-55934400	Flanking Active TSS	Fetal Thymus	thymus
45	chrX:55934200-55934400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chrX:55934200-55934600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chrX:55934200-55934600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chrX:55934200-55934600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chrX:55934200-55934600	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chrX:55934200-55934600	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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