Variant report

Variant	rs2664161
Chromosome Location	chrX:154031010-154031011
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	UBTF	chrX:154029995-154031064	K562	blood:	n/a	n/a
2	POLR2A	chrX:154027213-154031844	K562	blood:	n/a	n/a
3	POLR2A	chrX:154027279-154034457	PBDE	blood:	n/a	n/a
4	IRF1	chrX:154030021-154031294	K562	blood:	n/a	chrX:154031083-154031094 chrX:154031081-154031095 chrX:154031140-154031147 chrX:154031083-154031093 chrX:154031079-154031093 chrX:154031080-154031094 chrX:154031083-154031097 chrX:154031088-154031095

No.	Distal block	Cell Line	Cell type
1	chrX:154019167..154022429-chrX:154030729..154034585,3	MCF-7	breast:
2	X:153719993-153730954..X:154027387-154034565	K562	blood:
3	chrX:154028001..154031077-chrX:154031198..154034982,5	MCF-7	breast:
4	X:153614328-153625659..X:154027387-154034565	K562	blood:
5	chrX:154030621..154032461-chrX:154254105..154256936,2	K562	blood:

Variant related genes	Relation type
MPP1	TF binding region
ENSG00000264783	Chromatin interaction
ENSG00000165775	Chromatin interaction
ENSG00000185010	Chromatin interaction
ENSG00000130830	Chromatin interaction
ENSG00000264484	Chromatin interaction
ENSG00000264631	Chromatin interaction
ENSG00000147403	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1050705	1.00[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap]
rs1126762	0.81[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs1472977	1.00[ASW][hapmap];0.88[CHB][hapmap];0.94[GIH][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap]
rs17051889	1.00[CEU][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap]
rs1848762	0.81[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs2048294	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2221730	0.81[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs2664167	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2728538	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap]
rs4074307	1.00[ASW][hapmap];0.81[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap]
rs4898352	1.00[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap]
rs4898396	0.81[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs4898398	0.84[GIH][hapmap]
rs5945250	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap]
rs5986902	1.00[CEU][hapmap]
rs5987077	0.89[CHD][hapmap];0.82[GIH][hapmap]
rs6643622	1.00[CHD][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2664161	PLXNA3	cis	multi-tissue	Pritchard

Chromatin state (count:87 , 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:154006200-154033200	Weak transcription	Aorta	Aorta
3	chrX:154009800-154031800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chrX:154010800-154032800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chrX:154023600-154032800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chrX:154026600-154032000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chrX:154027200-154032800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chrX:154027400-154031600	Enhancers	Fetal Intestine Small	intestine
9	chrX:154027400-154032600	Enhancers	Primary T cells from cord blood	blood
10	chrX:154027800-154031200	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chrX:154027800-154032400	Enhancers	HepG2	liver
12	chrX:154028000-154033000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chrX:154028200-154032200	Weak transcription	Colonic Mucosa	Colon
14	chrX:154028200-154032600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chrX:154028200-154032600	Weak transcription	Esophagus	oesophagus
16	chrX:154028200-154032800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chrX:154028400-154032000	Weak transcription	Fetal Heart	heart
18	chrX:154028400-154032800	Weak transcription	Fetal Muscle Trunk	muscle
19	chrX:154028400-154033000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chrX:154028600-154031400	Enhancers	Fetal Thymus	thymus
21	chrX:154028600-154032000	Weak transcription	Right Atrium	heart
22	chrX:154028600-154032600	Weak transcription	Osteobl	bone
23	chrX:154028600-154032800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chrX:154028600-154032800	Weak transcription	NH-A	brain
25	chrX:154028800-154032400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chrX:154028800-154032400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chrX:154028800-154032600	Weak transcription	Right Ventricle	heart
28	chrX:154028800-154032800	Weak transcription	Psoas Muscle	Psoas
29	chrX:154028800-154032800	Weak transcription	NHDF-Ad	bronchial
30	chrX:154029000-154032200	Enhancers	Dnd41	blood
31	chrX:154029000-154032400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chrX:154029000-154032400	Weak transcription	NHLF	lung
33	chrX:154029000-154032600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chrX:154029000-154032600	Weak transcription	Brain Cingulate Gyrus	brain
35	chrX:154029000-154032600	Weak transcription	Brain Substantia Nigra	brain
36	chrX:154029000-154032600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chrX:154029000-154032600	Weak transcription	Fetal Muscle Leg	muscle
38	chrX:154029000-154032600	Weak transcription	Hela-S3	cervix
39	chrX:154029000-154032800	Weak transcription	Left Ventricle	heart
40	chrX:154029000-154032800	Weak transcription	HSMM	muscle
41	chrX:154029200-154031400	Enhancers	Primary hematopoietic stem cells	blood
42	chrX:154029200-154031400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chrX:154029200-154032200	Weak transcription	Colon Smooth Muscle	Colon
44	chrX:154029200-154032400	Weak transcription	Brain Anterior Caudate	brain
45	chrX:154029200-154032400	Weak transcription	Brain Hippocampus Middle	brain
46	chrX:154029200-154032600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chrX:154029200-154032600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chrX:154029200-154032600	Weak transcription	GM12878-XiMat	blood
49	chrX:154029200-154033000	Weak transcription	Spleen	Spleen
50	chrX:154029400-154031200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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