Variant report

Variant	rs5940453
Chromosome Location	chrX:154445759-154445760
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	REST	chrX:154444097-154445822	H1-neurons	neurons:	n/a	chrX:154445071-154445084 chrX:154444941-154444949
2	CEBPB	chrX:154444751-154445988	Hela-S3	cervix:	n/a	chrX:154445882-154445891 chrX:154445882-154445891
3	CTCF	chrX:154443939-154445869	A549	lung:	n/a	chrX:154445159-154445177 chrX:154445165-154445174

No.	Distal block	Cell Line	Cell type
1	chrX:154439521..154442406-chrX:154443106..154447353,6	K562	blood:
2	chrX:154438442..154440385-chrX:154445237..154447787,2	MCF-7	breast:
3	chrX:154444639..154446602-chrX:154492705..154495023,2	MCF-7	breast:
4	chrX:154299870..154302217-chrX:154444553..154446878,2	MCF-7	breast:
5	chrX:154255047..154257096-chrX:154443913..154445794,2	MCF-7	breast:
6	chrX:154440008..154442406-chrX:154443755..154447353,4	K562	blood:
7	chrX:154441104..154443352-chrX:154443765..154447008,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224978	TF binding region
ENSG00000185010	Chromatin interaction
ENSG00000155961	Chromatin interaction
ENSG00000165775	Chromatin interaction
ENSG00000185515	Chromatin interaction
ENSG00000224978	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1128863	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs12387365	1.00[CEU][hapmap]
rs17052027	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs28370194	1.00[ASW][hapmap]
rs3599	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs5940367	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs5987093	1.00[CEU][hapmap];0.87[TSI][hapmap]

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	nsv916671	chrX:154418093-154560374	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv532966	chrX:154418093-154721378	Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv29972	chrX:154418093-154929412	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv532965	chrX:154418093-155226096	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv532967	chrX:154418093-155252027	Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:154443800-154445800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chrX:154443800-154446000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chrX:154443800-154446000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chrX:154443800-154446000	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chrX:154443800-154446000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
6	chrX:154443800-154446000	Active TSS	GM12878-XiMat	blood
7	chrX:154443800-154446400	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chrX:154443800-154446400	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chrX:154443800-154446400	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chrX:154443800-154446400	Active TSS	HSMMtube	muscle
11	chrX:154444000-154445800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chrX:154444000-154445800	Active TSS	Brain Substantia Nigra	brain
13	chrX:154444000-154445800	Active TSS	Fetal Intestine Small	intestine
14	chrX:154444000-154445800	Active TSS	NHDF-Ad	bronchial
15	chrX:154444000-154445800	Active TSS	Osteobl	bone
16	chrX:154444000-154446000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chrX:154444000-154446000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chrX:154444000-154446000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chrX:154444000-154446000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chrX:154444000-154446000	Active TSS	Brain Angular Gyrus	brain
21	chrX:154444000-154446000	Active TSS	Brain Germinal Matrix	brain
22	chrX:154444000-154446000	Active TSS	Brain Hippocampus Middle	brain
23	chrX:154444000-154446000	Active TSS	Brain Inferior Temporal Lobe	brain
24	chrX:154444000-154446000	Active TSS	Colonic Mucosa	Colon
25	chrX:154444000-154446000	Active TSS	Duodenum Mucosa	Duodenum
26	chrX:154444000-154446000	Active TSS	Fetal Brain Male	brain
27	chrX:154444000-154446000	Active TSS	Fetal Kidney	kidney
28	chrX:154444000-154446000	Active TSS	Fetal Stomach	stomach
29	chrX:154444000-154446000	Active TSS	Rectal Mucosa Donor 31	rectum
30	chrX:154444000-154446000	Active TSS	NH-A	brain
31	chrX:154444000-154446200	Active TSS	H1 Cell Line	embryonic stem cell
32	chrX:154444000-154446200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chrX:154444000-154446200	Active TSS	Brain Anterior Caudate	brain
34	chrX:154444000-154446200	Active TSS	HSMM	muscle
35	chrX:154444000-154446400	Active TSS	H9 Cell Line	embryonic stem cell
36	chrX:154444000-154446400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chrX:154444000-154446400	Active TSS	Muscle Satellite Cultured Cells	--
38	chrX:154444000-154446400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chrX:154444000-154446400	Active TSS	Stomach Smooth Muscle	stomach
40	chrX:154444000-154446400	Active TSS	HMEC	breast
41	chrX:154444000-154446600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chrX:154444000-154446600	Active TSS	Fetal Brain Female	brain
43	chrX:154444000-154447200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chrX:154444200-154445800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chrX:154444200-154445800	Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chrX:154444200-154445800	Active TSS	Fetal Lung	lung
47	chrX:154444200-154445800	Active TSS	Fetal Muscle Trunk	muscle
48	chrX:154444200-154445800	Active TSS	Psoas Muscle	Psoas
49	chrX:154444200-154446000	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chrX:154444200-154446000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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