Variant report

Variant	rs5986981
Chromosome Location	chrX:153697347-153697348
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chrX:153697285-153697567	HepG2	liver:	n/a	n/a
2	NR3C1	chrX:153697280-153697724	A549	lung:	n/a	n/a
3	NR3C1	chrX:153697247-153697605	A549	lung:	n/a	n/a
4	NR3C1	chrX:153697278-153697745	A549	lung:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chrX:153597634..153602392-chrX:153694750..153697416,5	K562	blood:
2	chrX:153625628..153632278-chrX:153692369..153698999,8	K562	blood:
3	chrX:153625816..153632596-chrX:153691104..153698525,12	K562	blood:
4	X:153614328-153625659..X:153681712-153701576	Hela-S3	cervix:
5	X:153681712-153701576..X:153719993-153730954	Hela-S3	cervix:
6	chrX:153697091..153700406-chrX:153716936..153720236,4	MCF-7	breast:
7	chrX:153695809..153698632-chrX:153704638..153707837,4	K562	blood:
8	chrX:153605136..153607876-chrX:153696508..153698481,3	MCF-7	breast:
9	X:153657611-153671976..X:153681712-153701576	Hela-S3	cervix:

No data

Variant related genes	Relation type
PLXNA3	TF binding region
ENSG00000102119	Chromatin interaction
ENSG00000126903	Chromatin interaction
ENSG00000196976	Chromatin interaction
ENSG00000013563	Chromatin interaction
ENSG00000203879	Chromatin interaction
ENSG00000264631	Chromatin interaction
ENSG00000071553	Chromatin interaction
ENSG00000196924	Chromatin interaction
ENSG00000207165	Chromatin interaction
ENSG00000264783	Chromatin interaction
ENSG00000264484	Chromatin interaction
ENSG00000147403	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1050047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs12392447	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap]
rs2071429	0.82[CEU][hapmap]
rs2315325	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs2472393	0.82[CEU][hapmap]
rs4542114	0.86[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4898389	0.82[CEU][hapmap]
rs5945100	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs5945195	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs5945429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap]
rs5945431	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs5945433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5945434	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap]
rs5986979	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap]
rs5987266	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs5987267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7051615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs7057286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs7886727	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][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:110 , 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:153687600-153706600	Weak transcription	Psoas Muscle	Psoas
5	chrX:153687800-153706400	Weak transcription	A549	lung
6	chrX:153688000-153706600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chrX:153688000-153706600	Weak transcription	Fetal Kidney	kidney
8	chrX:153688200-153698200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chrX:153688200-153705200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chrX:153688200-153706400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chrX:153688400-153700000	Weak transcription	HepG2	liver
12	chrX:153688400-153701000	Weak transcription	Stomach Mucosa	stomach
13	chrX:153688400-153702200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chrX:153688400-153702400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chrX:153688400-153702800	ZNF genes & repeats	Fetal Stomach	stomach
16	chrX:153688400-153705400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chrX:153688400-153706400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chrX:153688400-153706400	Weak transcription	HMEC	breast
19	chrX:153688400-153706600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chrX:153688400-153706600	Weak transcription	HUVEC	blood vessel
21	chrX:153688600-153702400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chrX:153688600-153705400	Weak transcription	K562	blood
23	chrX:153688600-153705600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chrX:153688800-153698400	Weak transcription	NH-A	brain
25	chrX:153688800-153700400	Strong transcription	Fetal Intestine Large	intestine
26	chrX:153688800-153700400	Strong transcription	Fetal Intestine Small	intestine
27	chrX:153688800-153700400	Strong transcription	Thymus	Thymus
28	chrX:153688800-153702000	Strong transcription	Gastric	stomach
29	chrX:153688800-153702000	Strong transcription	Spleen	Spleen
30	chrX:153688800-153702200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chrX:153688800-153702200	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chrX:153688800-153702800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chrX:153688800-153706400	Weak transcription	HSMMtube	muscle
34	chrX:153689000-153699600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chrX:153689000-153700200	Strong transcription	Adipose Nuclei	Adipose
36	chrX:153689000-153701000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chrX:153689000-153701000	Strong transcription	Fetal Muscle Leg	muscle
38	chrX:153689000-153702000	Strong transcription	NHLF	lung
39	chrX:153689000-153702800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chrX:153689200-153700400	Strong transcription	Duodenum Mucosa	Duodenum
41	chrX:153689200-153700800	Strong transcription	Pancreas	Pancrea
42	chrX:153689200-153701800	Strong transcription	Esophagus	oesophagus
43	chrX:153689200-153702600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chrX:153689200-153702800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chrX:153689200-153702800	Strong transcription	Fetal Muscle Trunk	muscle
46	chrX:153689200-153706400	Weak transcription	NHDF-Ad	bronchial
47	chrX:153689400-153699400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chrX:153689400-153700000	Strong transcription	Placenta Amnion	Placenta Amnion
49	chrX:153689400-153700200	Strong transcription	Primary T cells fromperipheralblood	blood
50	chrX:153689400-153702400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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