Variant report

Variant	rs5945431
Chromosome Location	chrX:153701716-153701717
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chrX:153699604..153702122-chrX:153742862..153744546,2	MCF-7	breast:
2	chrX:153597195..153601946-chrX:153697915..153702072,4	MCF-7	breast:
3	X:153657611-153671976..X:153701576-153715648	Hela-S3	cervix:
4	chrX:153671344..153673711-chrX:153700353..153702824,2	MCF-7	breast:
5	chrX:153593549..153595758-chrX:153701522..153703850,2	MCF-7	breast:
6	chrX:153697571..153703616-chrX:153709529..153715825,8	MCF-7	breast:
7	chrX:153685935..153691133-chrX:153699303..153703882,6	K562	blood:
8	chrX:153605615..153607885-chrX:153700226..153701918,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000203879	Chromatin interaction
ENSG00000102119	Chromatin interaction
ENSG00000130827	Chromatin interaction
ENSG00000071889	Chromatin interaction
ENSG00000196924	Chromatin interaction
ENSG00000071859	Chromatin interaction
ENSG00000102178	Chromatin interaction
ENSG00000071553	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];0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs12392447	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap]
rs2071429	0.82[CEU][hapmap]
rs2315325	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs2472393	0.82[CEU][hapmap]
rs4542114	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.86[CHB][hapmap]
rs5945429	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap]
rs5945433	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs5945434	0.86[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap]
rs5986979	0.86[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap]
rs5986981	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs5987266	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs5987267	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7051615	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs7057286	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs7886727	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[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:107 , 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:153688200-153705200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chrX:153688200-153706400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chrX:153688400-153702200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chrX:153688400-153702400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chrX:153688400-153702800	ZNF genes & repeats	Fetal Stomach	stomach
13	chrX:153688400-153705400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chrX:153688400-153706400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chrX:153688400-153706400	Weak transcription	HMEC	breast
16	chrX:153688400-153706600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chrX:153688400-153706600	Weak transcription	HUVEC	blood vessel
18	chrX:153688600-153702400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chrX:153688600-153705400	Weak transcription	K562	blood
20	chrX:153688600-153705600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chrX:153688800-153702000	Strong transcription	Gastric	stomach
22	chrX:153688800-153702000	Strong transcription	Spleen	Spleen
23	chrX:153688800-153702200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chrX:153688800-153702200	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chrX:153688800-153702800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chrX:153688800-153706400	Weak transcription	HSMMtube	muscle
27	chrX:153689000-153702000	Strong transcription	NHLF	lung
28	chrX:153689000-153702800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chrX:153689200-153701800	Strong transcription	Esophagus	oesophagus
30	chrX:153689200-153702600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chrX:153689200-153702800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chrX:153689200-153702800	Strong transcription	Fetal Muscle Trunk	muscle
33	chrX:153689200-153706400	Weak transcription	NHDF-Ad	bronchial
34	chrX:153689400-153702400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chrX:153689400-153706000	Weak transcription	HSMM	muscle
36	chrX:153689600-153702200	Strong transcription	Right Ventricle	heart
37	chrX:153689600-153702400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chrX:153690000-153702800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chrX:153691000-153702400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chrX:153691200-153702600	Strong transcription	Brain Germinal Matrix	brain
41	chrX:153691400-153702400	Strong transcription	Stomach Smooth Muscle	stomach
42	chrX:153694200-153706200	Weak transcription	Rectal Smooth Muscle	rectum
43	chrX:153695000-153702600	Strong transcription	Muscle Satellite Cultured Cells	--
44	chrX:153695200-153706800	Weak transcription	Small Intestine	intestine
45	chrX:153696600-153702800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chrX:153697000-153702600	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chrX:153697400-153705000	Weak transcription	Fetal Thymus	thymus
48	chrX:153698200-153706400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chrX:153698400-153702200	Strong transcription	NH-A	brain
50	chrX:153699000-153702400	Strong transcription	Placenta	Placenta

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