Variant report

Variant	rs12395539
Chromosome Location	chrX:138285936-138285937
allele	A/G
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	POLR2A	chrX:138285442-138287746	MCF-7	breast:	n/a	n/a
2	CTCF	chrX:138285920-138286070	HRPEpiC	eye:	n/a	n/a
3	POLR2A	chrX:138285813-138286685	MCF-7	breast:	n/a	n/a
4	POLR2A	chrX:138285842-138286381	K562	blood:	n/a	n/a
5	NR2F2	chrX:138285827-138286258	MCF-7	breast:	n/a	chrX:138286095-138286110
6	E2F6	chrX:138285774-138286805	K562	blood:	n/a	chrX:138286420-138286430 chrX:138286414-138286424 chrX:138286150-138286159 chrX:138286417-138286427 chrX:138286169-138286180
7	REST	chrX:138285098-138287705	H1-neurons	neurons:	n/a	chrX:138285921-138285934 chrX:138287111-138287131 chrX:138287233-138287246 chrX:138285181-138285194 chrX:138285745-138285758 chrX:138285179-138285189
8	CTCF	chrX:138285887-138286030	MCF-7	breast:	n/a	n/a
9	CTCF	chrX:138285912-138286237	K562	blood:	n/a	chrX:138286141-138286154 chrX:138286141-138286154
10	CTCF	chrX:138285900-138286050	K562	blood:	n/a	n/a
11	E2F6	chrX:138285696-138286579	H1-hESC	embryonic stem cell:	n/a	chrX:138286420-138286430 chrX:138286414-138286424 chrX:138285744-138285753 chrX:138286150-138286159 chrX:138285744-138285756 chrX:138286417-138286427 chrX:138286169-138286180
12	MYC	chrX:138285797-138286058	MCF-7	breast:	n/a	n/a
13	SPI1	chrX:138285850-138286070	K562	blood:	n/a	n/a
14	MAX	chrX:138285835-138286309	K562	blood:	n/a	n/a
15	RCOR1	chrX:138285832-138286375	K562	blood:	n/a	n/a
16	CTBP2	chrX:138284616-138286747	H1-hESC	embryonic stem cell:	n/a	n/a
17	NR2F2	chrX:138285899-138286245	K562	blood:	n/a	chrX:138286095-138286110
18	CTCF	chrX:138285880-138286030	NHDF-neo	bronchial:	n/a	n/a
19	CTCF	chrX:138285840-138285990	NHDF-neo	bronchial:	n/a	n/a
20	MAX	chrX:138285673-138286512	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chrX:138285837-138286107	ProgFib	skin:	n/a	n/a
22	ZBTB7A	chrX:138285889-138286196	K562	blood:	n/a	chrX:138286165-138286174
23	SIN3A	chrX:138285315-138286437	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chrX:138285873-138287837	K562	blood:	n/a	n/a
25	CTCF	chrX:138285906-138286233	MCF-7	breast:	n/a	chrX:138286141-138286154 chrX:138286141-138286154
26	ZNF143	chrX:138285867-138286206	H1-hESC	embryonic stem cell:	n/a	chrX:138286021-138286040
27	POLR2A	chrX:138285798-138287834	K562	blood:	n/a	n/a
28	CTCF	chrX:138285900-138286086	Pancreas_OC	pancreas:	n/a	n/a
29	CTCF	chrX:138285824-138286263	MCF-7	breast:	n/a	chrX:138286141-138286154 chrX:138286141-138286154
30	CTCF	chrX:138285880-138286030	HBMEC	blood vessel:	n/a	n/a
31	POLR2A	chrX:138285167-138286591	H1-neurons	neurons:	n/a	n/a
32	E2F6	chrX:138285865-138286519	H1-hESC	embryonic stem cell:	n/a	chrX:138286420-138286430 chrX:138286414-138286424 chrX:138286150-138286159 chrX:138286417-138286427 chrX:138286169-138286180
33	E2F6	chrX:138285475-138286767	K562	blood:	n/a	chrX:138286420-138286430 chrX:138286414-138286424 chrX:138285744-138285753 chrX:138286150-138286159 chrX:138285744-138285756 chrX:138286417-138286427 chrX:138285550-138285560 chrX:138286169-138286180
34	POLR2A	chrX:138285607-138286411	H1-neurons	neurons:	n/a	n/a
35	MAZ	chrX:138285771-138286321	K562	blood:	n/a	n/a
36	CTCF	chrX:138285870-138286120	A549	lung:	n/a	n/a
37	CTCF	chrX:138285840-138285990	HAc	cerebellar:	n/a	n/a
38	NR2F2	chrX:138285895-138286345	MCF-7	breast:	n/a	chrX:138286095-138286110
39	CTCF	chrX:138285828-138286253	MCF-7	breast:	n/a	chrX:138286141-138286154 chrX:138286141-138286154
40	MAX	chrX:138285689-138286558	K562	blood:	n/a	n/a
41	HMGN3	chrX:138285762-138286638	K562	blood:	n/a	n/a
42	SPI1	chrX:138285896-138286058	K562	blood:	n/a	n/a
43	TBP	chrX:138285839-138286431	K562	blood:	n/a	n/a
44	CTCF	chrX:138285868-138286204	H1-hESC	embryonic stem cell:	n/a	chrX:138286141-138286154 chrX:138286141-138286154
45	CTCF	chrX:138285900-138286050	AG09319	gingival:	n/a	n/a
46	MAX	chrX:138285770-138286592	A549	lung:	n/a	n/a
47	CTCF	chrX:138285920-138286070	MCF-7	breast:	n/a	n/a
48	CTCF	chrX:138285880-138286030	GM12865	blood:	n/a	n/a
49	BHLHE40	chrX:138285845-138286260	K562	blood:	n/a	n/a
50	CTCF	chrX:138285920-138286070	HEK293	kidney:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chrX:138285922-138285972	GM12878	blood:	n/a
2	chrX:138285922-138285972	GM19239	blood:	n/a
3	chrX:138285922-138285972	NH-A	brain:	n/a
4	chrX:138285922-138285972	SAEC	small airway:	n/a
5	chrX:138285922-138285972	Hepatocyte	liver:	n/a
6	chrX:138285922-138285972	HNPCEpiC	eye:	n/a
7	chrX:138285922-138285972	HEK293	kidney:	embryo
8	chrX:138285922-138285972	RPTEC	kidney:	n/a
9	chrX:138285922-138285972	HPAEpiC	pulmonary alveolar:	n/a
10	chrX:138285922-138285972	MCF10A-Er-Src	breast:	n/a
11	chrX:138285922-138285972	HMEC	breast:	n/a
12	chrX:138285922-138285972	ECC-1	luminal epithelium:	n/a
13	chrX:138285922-138285972	T-47D	breast:	n/a
14	chrX:138285922-138285972	A549	lung:	n/a
15	chrX:138285922-138285972	NT2-D1	testis:	n/a
16	chrX:138285922-138285972	CMK	blood:	n/a
17	chrX:138285922-138285972	HRPEpiC	eye:	n/a
18	chrX:138285922-138285972	HCF	heart:	n/a
19	chrX:138285922-138285972	PANC-1	pancreas:	n/a
20	chrX:138285922-138285972	AG10803	skin:	n/a
21	chrX:138285922-138285972	ovcar-3	ovarian:	n/a
22	chrX:138285922-138285972	Caco-2	colon:	n/a
23	chrX:138285922-138285972	ProgFib	skin:	n/a
24	chrX:138285922-138285972	GM12892	blood:	n/a
25	chrX:138285922-138285972	AG04450	lung:	fetal
26	chrX:138285922-138285972	HRCEpiC	kidney:	n/a
27	chrX:138285922-138285972	BE2_C	brain:	n/a
28	chrX:138285922-138285972	GM06990	blood:	n/a
29	chrX:138285922-138285972	U87	brain:	n/a
30	chrX:138285922-138285972	NHBE	bronchial:	n/a
31	chrX:138285922-138285972	HCM	heart:	n/a
32	chrX:138285922-138285972	H1-hESC	embryonic stem cell:	embryo
33	chrX:138285922-138285972	Jurkat	blood:	n/a
34	chrX:138285922-138285972	SK-N-MC	brain:	n/a
35	chrX:138285922-138285972	HRE	kidney:	n/a
36	chrX:138285922-138285972	HepG2	liver:	n/a
37	chrX:138285922-138285972	GM12891	blood:	n/a
38	chrX:138285922-138285972	HL-60	blood:	n/a
39	chrX:138285922-138285972	SK-N-SH_RA	brain:	n/a
40	chrX:138285922-138285972	BJ	skin:	n/a
41	chrX:138285922-138285972	NHDF-neo	bronchial:	n/a
42	chrX:138285922-138285972	AG09319	gingival:	n/a
43	chrX:138285922-138285972	SK-N-SH	brain:	n/a
44	chrX:138285922-138285972	AG04449	skin:	fetal
45	chrX:138285922-138285972	MCF-7	breast:	n/a
46	chrX:138285922-138285972	HAEpiC	amniotic membrane:	n/a
47	chrX:138285922-138285972	PrEC	prostate:	n/a
48	chrX:138285922-138285972	Hela-S3	cervix:	n/a
49	chrX:138285922-138285972	PFSK-1	brain:	n/a
50	chrX:138285922-138285972	AG09309	skin:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:138285411..138288031-chrX:138303226..138305707,3	K562	blood:

Variant related genes	Relation type
FGF13	TF binding region
FGF13	CpG island
ENSG00000129682	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525867	chrX:137580983-138439843	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv533984	chrX:137938683-138556308	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv532935	chrX:138281469-138764448	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv3346694	chrX:138283686-138289084	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv3447668	chrX:138284786-138286884	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:138277600-138286000	Weak transcription	Right Atrium	heart
2	chrX:138283000-138288600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chrX:138284400-138287800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chrX:138284400-138288400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
5	chrX:138284600-138286400	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chrX:138284600-138287800	Bivalent/Poised TSS	Fetal Brain Female	brain
7	chrX:138284600-138288000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
8	chrX:138284600-138288200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chrX:138284600-138288600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chrX:138284600-138288800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
11	chrX:138284600-138288800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chrX:138284800-138286000	Bivalent/Poised TSS	Placenta	Placenta
13	chrX:138284800-138287800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chrX:138284800-138287800	Active TSS	K562	blood
15	chrX:138284800-138288000	Active TSS	Psoas Muscle	Psoas
16	chrX:138284800-138288400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
17	chrX:138284800-138288600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
18	chrX:138285000-138286200	Enhancers	Spleen	Spleen
19	chrX:138285000-138286400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chrX:138285000-138287400	Active TSS	NH-A	brain
21	chrX:138285000-138287800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chrX:138285200-138286000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chrX:138285200-138286000	Enhancers	Pancreas	Pancrea
24	chrX:138285200-138286400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chrX:138285200-138286400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
26	chrX:138285200-138287000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
27	chrX:138285200-138287000	Bivalent/Poised TSS	Colonic Mucosa	Colon
28	chrX:138285200-138287600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
29	chrX:138285200-138287800	Active TSS	Brain Anterior Caudate	brain
30	chrX:138285200-138287800	Active TSS	Brain Germinal Matrix	brain
31	chrX:138285200-138288000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chrX:138285200-138288400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chrX:138285200-138288600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
34	chrX:138285400-138286000	Bivalent/Poised TSS	Adipose Nuclei	Adipose
35	chrX:138285400-138286000	Bivalent Enhancer	Lung	lung
36	chrX:138285400-138286000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
37	chrX:138285400-138286400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
38	chrX:138285400-138287600	Active TSS	Esophagus	oesophagus
39	chrX:138285400-138287600	Active TSS	Gastric	stomach
40	chrX:138285400-138287800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chrX:138285400-138288000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chrX:138285400-138288000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chrX:138285400-138288000	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
44	chrX:138285400-138288000	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
45	chrX:138285400-138288000	Active TSS	Ovary	ovary
46	chrX:138285400-138288000	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chrX:138285600-138287000	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
48	chrX:138285600-138287800	Bivalent/Poised TSS	Fetal Stomach	stomach
49	chrX:138285600-138288000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chrX:138285600-138288000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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