Variant report

Variant	rs5986979
Chromosome Location	chrX:153690397-153690398
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chrX:153690367-153690417	ProgFib	skin:	n/a
2	chrX:153690367-153690417	SAEC	small airway:	n/a
3	chrX:153690367-153690417	HCT-116	colon:	n/a
4	chrX:153690367-153690417	A549	lung:	n/a
5	chrX:153690367-153690417	NT2-D1	testis:	n/a
6	chrX:153690367-153690417	U87	brain:	n/a
7	chrX:153690367-153690417	ECC-1	luminal epithelium:	n/a
8	chrX:153690367-153690417	AG10803	skin:	n/a
9	chrX:153690367-153690417	HL-60	blood:	n/a
10	chrX:153690367-153690417	BJ	skin:	n/a
11	chrX:153690367-153690417	HEEpiC	esophagus:	n/a
12	chrX:153690367-153690417	ovcar-3	ovarian:	n/a
13	chrX:153690367-153690417	IMR90	lung:	fetal
14	chrX:153690367-153690417	GM12891	blood:	n/a
15	chrX:153690367-153690417	NH-A	brain:	n/a
16	chrX:153690367-153690417	HRCEpiC	kidney:	n/a
17	chrX:153690367-153690417	PrEC	prostate:	n/a
18	chrX:153690367-153690417	HCM	heart:	n/a
19	chrX:153690367-153690417	NB4	blood:	n/a
20	chrX:153690367-153690417	AG04449	skin:	fetal
21	chrX:153690367-153690417	T-47D	breast:	n/a
22	chrX:153690367-153690417	HCPEpiC	choroid plexus:	n/a
23	chrX:153690367-153690417	SK-N-MC	brain:	n/a
24	chrX:153690367-153690417	SK-N-SH	brain:	n/a
25	chrX:153690367-153690417	GM06990	blood:	n/a
26	chrX:153690367-153690417	MCF10A-Er-Src	breast:	n/a
27	chrX:153690367-153690417	HMEC	breast:	n/a
28	chrX:153690367-153690417	SKMC	muscle:	n/a
29	chrX:153690367-153690417	MCF-7	breast:	n/a
30	chrX:153690367-153690417	HRPEpiC	eye:	n/a
31	chrX:153690367-153690417	PANC-1	pancreas:	n/a
32	chrX:153690367-153690417	LNCaP	prostate:	n/a
33	chrX:153690367-153690417	NHDF-neo	bronchial:	n/a
34	chrX:153690367-153690417	GM12892	blood:	n/a
35	chrX:153690367-153690417	NHBE	bronchial:	n/a
36	chrX:153690367-153690417	AoSMC	blood vessel:	n/a
37	chrX:153690367-153690417	RPTEC	kidney:	n/a
38	chrX:153690367-153690417	Hela-S3	cervix:	n/a
39	chrX:153690367-153690417	GM12878	blood:	n/a
40	chrX:153690367-153690417	Caco-2	colon:	n/a
41	chrX:153690367-153690417	H1-hESC	embryonic stem cell:	embryo
42	chrX:153690367-153690417	AG04450	lung:	fetal
43	chrX:153690367-153690417	HRE	kidney:	n/a
44	chrX:153690367-153690417	HCF	heart:	n/a
45	chrX:153690367-153690417	HNPCEpiC	eye:	n/a
46	chrX:153690367-153690417	PFSK-1	brain:	n/a
47	chrX:153690367-153690417	AG09319	gingival:	n/a
48	chrX:153690367-153690417	HIPEpiC	eye:	n/a
49	chrX:153690367-153690417	HEK293	kidney:	embryo
50	chrX:153690367-153690417	HUVEC	blood vessel:	n/a

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chrX:153685519..153691890-chrX:153703911..153708727,11	K562	blood:
2	chrX:153625623..153631615-chrX:153684928..153690706,13	K562	blood:
3	chrX:153624950..153633168-chrX:153684275..153690571,17	MCF-7	breast:
4	X:153614328-153625659..X:153681712-153701576	Hela-S3	cervix:
5	X:153681712-153701576..X:153719993-153730954	Hela-S3	cervix:
6	chrX:153670174..153672122-chrX:153688438..153690922,3	K562	blood:
7	chrX:153607504..153609243-chrX:153688583..153690655,2	MCF-7	breast:
8	X:153657611-153671976..X:153681712-153701576	Hela-S3	cervix:
9	chrX:153596642..153600094-chrX:153690004..153694161,3	K562	blood:
10	chrX:153625410..153630111-chrX:153684839..153690625,12	K562	blood:
11	chrX:153690244..153692522-chrX:153743699..153745930,2	K562	blood:

No data

Variant related genes	Relation type
PLXNA3	CpG island
ENSG00000264484	Chromatin interaction
ENSG00000071889	Chromatin interaction
ENSG00000196976	Chromatin interaction
ENSG00000071553	Chromatin interaction
ENSG00000264631	Chromatin interaction
ENSG00000196924	Chromatin interaction
ENSG00000264783	Chromatin interaction
ENSG00000203879	Chromatin interaction
ENSG00000147403	Chromatin interaction
ENSG00000013563	Chromatin interaction
ENSG00000207165	Chromatin interaction
ENSG00000102119	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1050047	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap]
rs12392447	1.00[CHB][hapmap]
rs2315325	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs4542114	0.86[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap]
rs5945195	1.00[CHB][hapmap]
rs5945429	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs5945431	0.86[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap]
rs5945433	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs5945434	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs5986981	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap]
rs5987266	0.82[JPT][hapmap]
rs5987267	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7051615	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap]
rs7057286	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap]
rs7886727	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33199	chrX:152864376-153820241	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	276 gene(s)	inside rSNPs	diseases
2	nsv528291	chrX:152864376-153827637	Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	277 gene(s)	inside rSNPs	diseases
3	nsv915605	chrX:153333946-153783638	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
4	nsv519042	chrX:153348431-153829693	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
5	nsv532962	chrX:153564946-153870337	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	199 gene(s)	inside rSNPs	diseases
6	nsv532963	chrX:153576890-153822717	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	195 gene(s)	inside rSNPs	diseases
7	nsv530281	chrX:153622940-153783184	Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
8	nsv532964	chrX:153622940-153854307	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:153686000-153702000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
2	chrX:153687000-153702400	ZNF genes & repeats	Fetal Brain Female	brain
3	chrX:153687400-153706600	Weak transcription	Liver	Liver
4	chrX:153687600-153691200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
5	chrX:153687600-153706600	Weak transcription	Psoas Muscle	Psoas
6	chrX:153687800-153706400	Weak transcription	A549	lung
7	chrX:153688000-153691000	Enhancers	Fetal Brain Male	brain
8	chrX:153688000-153691200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chrX:153688000-153691200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
10	chrX:153688000-153692800	Weak transcription	Fetal Lung	lung
11	chrX:153688000-153706600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chrX:153688000-153706600	Weak transcription	Fetal Kidney	kidney
13	chrX:153688200-153691400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chrX:153688200-153692000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chrX:153688200-153693400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chrX:153688200-153698200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chrX:153688200-153705200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chrX:153688200-153706400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chrX:153688400-153690600	Weak transcription	Ovary	ovary
20	chrX:153688400-153692200	Weak transcription	Primary B cells from cord blood	blood
21	chrX:153688400-153692400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chrX:153688400-153693000	Weak transcription	NHEK	skin
23	chrX:153688400-153693800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chrX:153688400-153693800	Weak transcription	Colon Smooth Muscle	Colon
25	chrX:153688400-153693800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chrX:153688400-153694200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chrX:153688400-153694200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chrX:153688400-153694800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chrX:153688400-153694800	Weak transcription	Small Intestine	intestine
30	chrX:153688400-153700000	Weak transcription	HepG2	liver
31	chrX:153688400-153701000	Weak transcription	Stomach Mucosa	stomach
32	chrX:153688400-153702200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chrX:153688400-153702400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chrX:153688400-153702800	ZNF genes & repeats	Fetal Stomach	stomach
35	chrX:153688400-153705400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chrX:153688400-153706400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chrX:153688400-153706400	Weak transcription	HMEC	breast
38	chrX:153688400-153706600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chrX:153688400-153706600	Weak transcription	HUVEC	blood vessel
40	chrX:153688600-153690400	Weak transcription	Left Ventricle	heart
41	chrX:153688600-153691200	Weak transcription	Primary B cells from peripheral blood	blood
42	chrX:153688600-153691200	Enhancers	Brain Hippocampus Middle	brain
43	chrX:153688600-153691800	Weak transcription	Right Atrium	heart
44	chrX:153688600-153692400	Weak transcription	Rectal Smooth Muscle	rectum
45	chrX:153688600-153694000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chrX:153688600-153694200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chrX:153688600-153694400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
48	chrX:153688600-153702400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chrX:153688600-153705400	Weak transcription	K562	blood
50	chrX:153688600-153705600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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