Variant report

Variant	rs11887
Chromosome Location	chrX:154467457-154467458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chrX:153779711..153781942-chrX:154465936..154467690,2	K562	blood:
2	chrX:154462893..154464786-chrX:154466274..154467936,2	MCF-7	breast:
3	chrX:154465478..154467613-chrX:154473128..154477235,3	K562	blood:

Variant related genes	Relation type
ENSG00000155959	Chromatin interaction
ENSG00000073009	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11156600	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs12013168	0.84[CEU][hapmap];0.89[CHB][hapmap]
rs1393999	0.91[CHB][hapmap]
rs3105275	0.85[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.94[MEX][hapmap]
rs3105276	0.85[CEU][hapmap];0.91[CHB][hapmap]
rs35296872	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[MEX][hapmap]
rs480210	0.87[ASW][hapmap];0.86[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.84[MEX][hapmap]
rs4893113	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs492622	0.85[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs496740	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs499428	0.85[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs499669	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[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs504984	0.85[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs507127	0.85[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs516396	0.84[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap]
rs519641	0.83[CEU][hapmap];0.89[CHB][hapmap]
rs520145	0.84[CEU][hapmap];0.91[CHB][hapmap]
rs523614	0.85[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs524609	0.85[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs525161	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs533001	0.85[CEU][hapmap];0.91[CHB][hapmap]
rs542899	0.85[CEU][hapmap];0.91[CHB][hapmap]
rs543054	0.85[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap]
rs544582	0.85[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs547724	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap]
rs559165	0.85[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs568396	0.85[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap]
rs573189	0.87[ASW][hapmap];0.86[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.94[MEX][hapmap]
rs573572	0.85[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs5945282	0.87[ASW][hapmap]
rs5945296	0.87[ASW][hapmap]
rs5983697	1.00[CHB][hapmap]
rs5983764	0.85[CEU][hapmap];0.91[CHB][hapmap]
rs5987090	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6567813	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap]
rs782769	0.85[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs965691	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv534387	chrX:154455491-154560375	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11887	TMLHE	cis	multi-tissue	Pritchard
rs11887	F8A1	cis	lymphoblastoid	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:154445600-154467800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chrX:154445600-154471800	Weak transcription	Aorta	Aorta
3	chrX:154446200-154468000	Weak transcription	Brain Substantia Nigra	brain
4	chrX:154446200-154469800	Weak transcription	Right Ventricle	heart
5	chrX:154446400-154467800	Weak transcription	Pancreas	Pancrea
6	chrX:154446400-154471400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chrX:154446400-154472000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chrX:154447200-154467600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chrX:154447200-154471600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chrX:154450800-154470200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chrX:154452800-154468400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chrX:154453200-154467800	Strong transcription	Dnd41	blood
13	chrX:154453200-154469200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chrX:154454400-154468600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chrX:154455000-154468200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chrX:154455600-154468400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chrX:154456800-154470000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chrX:154457600-154469600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chrX:154457600-154469800	Weak transcription	NHDF-Ad	bronchial
20	chrX:154457600-154471800	Weak transcription	NH-A	brain
21	chrX:154459400-154467800	Weak transcription	Fetal Brain Male	brain
22	chrX:154459400-154467800	Weak transcription	Psoas Muscle	Psoas
23	chrX:154461000-154467800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chrX:154461000-154468600	Strong transcription	Primary T cells fromperipheralblood	blood
25	chrX:154462800-154468200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chrX:154462800-154468600	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chrX:154463400-154471400	Weak transcription	Fetal Kidney	kidney
28	chrX:154463800-154468400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chrX:154464000-154468400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chrX:154464000-154469200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chrX:154464200-154467800	Strong transcription	Primary B cells from peripheral blood	blood
32	chrX:154464200-154467800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chrX:154464400-154467600	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chrX:154464400-154467800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chrX:154464400-154468200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
36	chrX:154464600-154467600	Strong transcription	Fetal Intestine Large	intestine
37	chrX:154464600-154467800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chrX:154464600-154468200	Strong transcription	Liver	Liver
39	chrX:154464600-154468600	Strong transcription	Fetal Thymus	thymus
40	chrX:154464800-154467800	Strong transcription	Placenta	Placenta
41	chrX:154464800-154468600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chrX:154465000-154467600	Strong transcription	Adipose Nuclei	Adipose
43	chrX:154465200-154467600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chrX:154465600-154468400	Strong transcription	K562	blood
45	chrX:154465600-154490800	Weak transcription	Primary T cells from cord blood	blood
46	chrX:154466000-154467600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chrX:154466200-154467800	Weak transcription	Brain Cingulate Gyrus	brain
48	chrX:154466200-154468600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chrX:154466200-154469600	Weak transcription	Brain Angular Gyrus	brain
50	chrX:154466200-154470000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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