Variant report

Variant	rs989711
Chromosome Location	chrX:154739500-154739501
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-F8A2-3	chrX:154739490-154739868	NONHSAT139242

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10782079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1084450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs473491	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap]
rs473529	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs473772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs476928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs479901	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs496740	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs498000	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs520145	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs524609	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs547724	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap]
rs561928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs568396	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs574386	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs580468	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap]
rs5940376	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.91[YRI][hapmap]
rs5940478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs5940479	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs5940484	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs5940486	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap]
rs5940510	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs5940539	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap]
rs5983658	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs5983743	0.91[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap]
rs5983764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs628761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs674707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs89278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[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	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
2	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
3	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
4	nsv915940	chrX:154577793-155232907	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer 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	22 gene(s)	inside rSNPs	diseases
5	nsv534441	chrX:154664337-155251871	Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv818043	chrX:154737376-154777564	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv519485	chrX:154737376-154929412	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv869305	chrX:154739403-155190347	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs989711	F8A1	cis	lymphoblastoid	seeQTL
rs989711	TMLHE	cis	multi-tissue	Pritchard
rs989711	TMLHE	cis	lymphoblastoid	seeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:154732600-154751800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chrX:154732600-154751800	Weak transcription	Brain Hippocampus Middle	brain
3	chrX:154732800-154740800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chrX:154732800-154740800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chrX:154732800-154751600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chrX:154732800-154752000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chrX:154732800-154752000	Weak transcription	Duodenum Mucosa	Duodenum
8	chrX:154733000-154742400	Weak transcription	A549	lung
9	chrX:154733200-154739600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chrX:154733400-154752000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chrX:154733600-154740800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chrX:154733600-154740800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chrX:154733800-154740800	Weak transcription	Primary T cells from cord blood	blood
14	chrX:154733800-154740800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chrX:154733800-154752000	Weak transcription	Brain Germinal Matrix	brain
16	chrX:154734000-154752000	Weak transcription	Placenta	Placenta
17	chrX:154734000-154754800	Weak transcription	Stomach Smooth Muscle	stomach
18	chrX:154734200-154740800	Weak transcription	Ovary	ovary
19	chrX:154734200-154740800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chrX:154734400-154742400	Weak transcription	K562	blood
21	chrX:154734400-154755800	Weak transcription	Thymus	Thymus
22	chrX:154734600-154742200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chrX:154734600-154757200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chrX:154734600-154777000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chrX:154735000-154743000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chrX:154735000-154752000	Weak transcription	Brain Anterior Caudate	brain
27	chrX:154735200-154740800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chrX:154735200-154740800	Weak transcription	Liver	Liver
29	chrX:154735200-154742400	Weak transcription	Brain Cingulate Gyrus	brain
30	chrX:154735200-154752000	Weak transcription	Fetal Thymus	thymus
31	chrX:154735200-154754000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chrX:154735200-154755200	Weak transcription	Rectal Smooth Muscle	rectum
33	chrX:154735400-154740800	Weak transcription	Left Ventricle	heart
34	chrX:154735400-154740800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chrX:154735400-154754800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chrX:154735400-154773800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chrX:154735600-154742400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chrX:154735800-154752000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chrX:154736000-154740800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chrX:154736000-154742200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chrX:154736400-154752200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chrX:154736600-154751800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chrX:154736800-154739600	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chrX:154736800-154740800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chrX:154736800-154740800	Weak transcription	Adipose Nuclei	Adipose
46	chrX:154736800-154752000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chrX:154737000-154740800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chrX:154737000-154740800	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chrX:154737200-154740800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chrX:154737400-154773400	Weak transcription	Placenta Amnion	Placenta Amnion

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