Variant report

Variant	rs2728538
Chromosome Location	chrX:154025165-154025166
allele	A/T
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	POLR2A	chrX:154024700-154027005	K562	blood:	n/a	n/a
2	POLR2A	chrX:154025155-154025266	GM12878	blood:	n/a	n/a
3	POLR2A	chrX:154025056-154025295	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:153978778..153980701-chrX:154024363..154026885,2	K562	blood:

Variant related genes	Relation type
MPP1	TF binding region
ENSG00000160219	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1050705	0.88[CHB][hapmap];0.94[CHD][hapmap]
rs1126762	0.87[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1472977	0.88[CHB][hapmap];0.85[MEX][hapmap]
rs1848762	0.87[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1848763	0.81[MEX][hapmap]
rs2048294	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2221730	0.87[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs2664161	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap]
rs2664167	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2664169	0.81[MEX][hapmap]
rs2664170	0.81[MEX][hapmap]
rs2728526	0.81[MEX][hapmap]
rs2728725	0.83[TSI][hapmap]
rs4074307	0.87[CHB][hapmap];0.94[CHD][hapmap]
rs4898352	0.88[CHB][hapmap];0.94[CHD][hapmap]
rs4898396	0.87[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs5945250	0.93[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap]
rs5986902	0.93[CEU][hapmap]
rs5987015	0.81[MEX][hapmap]
rs5987016	0.81[MEX][hapmap]
rs5987077	0.83[CHD][hapmap]
rs6643622	0.94[CHD][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2728538	PLXNA3	cis	multi-tissue	Pritchard

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:154004600-154032400	Weak transcription	Small Intestine	intestine
2	chrX:154005400-154027800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chrX:154005600-154028800	Weak transcription	Brain Anterior Caudate	brain
4	chrX:154005800-154027800	Weak transcription	Brain Cingulate Gyrus	brain
5	chrX:154006000-154027400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chrX:154006200-154028000	Weak transcription	Left Ventricle	heart
7	chrX:154006200-154033200	Weak transcription	Aorta	Aorta
8	chrX:154006400-154027200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chrX:154006400-154027800	Weak transcription	Esophagus	oesophagus
10	chrX:154008000-154027400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chrX:154008400-154025400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chrX:154008800-154027600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chrX:154009600-154027800	Weak transcription	Brain Hippocampus Middle	brain
14	chrX:154009800-154031800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chrX:154010000-154027800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chrX:154010000-154027800	Weak transcription	Stomach Smooth Muscle	stomach
17	chrX:154010000-154028000	Weak transcription	Fetal Intestine Large	intestine
18	chrX:154010000-154030200	Weak transcription	Lung	lung
19	chrX:154010400-154027400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chrX:154010800-154027400	Weak transcription	Brain Angular Gyrus	brain
21	chrX:154010800-154032800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chrX:154011000-154027200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chrX:154012400-154025200	Weak transcription	Primary B cells from cord blood	blood
24	chrX:154012800-154027400	Weak transcription	Primary T cells from cord blood	blood
25	chrX:154013200-154027200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chrX:154014600-154026000	Weak transcription	Thymus	Thymus
27	chrX:154014600-154026200	Weak transcription	Dnd41	blood
28	chrX:154014600-154027400	Weak transcription	Fetal Intestine Small	intestine
29	chrX:154014800-154027800	Weak transcription	Placenta	Placenta
30	chrX:154019600-154027800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chrX:154020800-154027600	Weak transcription	Duodenum Mucosa	Duodenum
32	chrX:154021800-154027400	Weak transcription	Liver	Liver
33	chrX:154022400-154026000	Enhancers	Fetal Thymus	thymus
34	chrX:154022400-154026200	Enhancers	Primary monocytes fromperipheralblood	blood
35	chrX:154022600-154025600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chrX:154022800-154027600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chrX:154022800-154027800	Enhancers	Monocytes-CD14+_RO01746	blood
38	chrX:154023200-154030200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chrX:154023400-154027600	Weak transcription	Pancreas	Pancrea
40	chrX:154023600-154032800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chrX:154024600-154025600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chrX:154024800-154025200	Weak transcription	Primary hematopoietic stem cells	blood
43	chrX:154024800-154025400	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chrX:154024800-154026200	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chrX:154024800-154027200	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chrX:154024800-154027400	Enhancers	A549	lung
47	chrX:154024800-154029600	Transcr. at gene 5' and 3'	K562	blood
48	chrX:154025000-154025400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chrX:154025000-154025800	Enhancers	Primary B cells from peripheral blood	blood
50	chrX:154025000-154025800	Enhancers	Primary T killer memory cells from peripheral blood	blood

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