Variant report

Variant	rs10800125
Chromosome Location	chr1:165628921-165628922
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:165618685..165622875-chr1:165623936..165629160,4	K562	blood:
2	chr1:165624974..165629115-chr1:165629566..165633277,5	K562	blood:

Variant related genes	Relation type
ENSG00000143198	Chromatin interaction
ENSG00000206990	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10494446	0.83[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs10494447	0.83[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.89[ASN][1000 genomes]
rs10800122	0.89[ASN][1000 genomes]
rs10800123	0.83[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.89[ASN][1000 genomes]
rs10800124	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800126	0.83[ASN][1000 genomes]
rs10918229	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs10918230	0.89[ASN][1000 genomes]
rs10918231	0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs10918232	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918233	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10918235	0.83[CHB][hapmap]
rs10918239	0.83[CHB][hapmap]
rs12065621	1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs12072628	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12072634	1.00[CHB][hapmap]
rs12080699	1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs12081903	1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs12084651	0.85[ASN][1000 genomes]
rs12122497	0.88[ASN][1000 genomes]
rs12123278	0.81[ASN][1000 genomes]
rs1538113	0.94[ASN][1000 genomes]
rs1878074	0.83[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.89[ASN][1000 genomes]
rs1878075	0.83[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2050619	0.83[CHB][hapmap]
rs2176151	0.81[ASN][1000 genomes]
rs2297762	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs2297763	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2348727	1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2348728	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2348729	0.81[ASN][1000 genomes]
rs3795540	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs3820362	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4147603	0.89[ASN][1000 genomes]
rs4147604	0.83[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs4147605	0.83[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.89[ASN][1000 genomes]
rs4147606	0.83[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs4147607	0.84[ASN][1000 genomes]
rs4147610	0.91[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs4147611	0.83[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.89[ASN][1000 genomes]
rs4539111	0.89[ASN][1000 genomes]
rs4581256	0.89[ASN][1000 genomes]
rs4638106	0.83[ASN][1000 genomes]
rs4646895	1.00[CHB][hapmap]
rs4646896	0.91[CHB][hapmap]
rs4646897	1.00[CHB][hapmap]
rs56279704	0.94[ASN][1000 genomes]
rs61800398	0.85[ASN][1000 genomes]
rs6683969	1.00[CHB][hapmap]
rs7525102	0.85[ASN][1000 genomes]
rs7534437	0.91[CHB][hapmap]
rs8133	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs884121	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9333483	0.83[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.89[ASN][1000 genomes]
rs9333489	0.89[ASN][1000 genomes]
rs9333490	0.89[ASN][1000 genomes]
rs9333494	0.89[ASN][1000 genomes]
rs9333496	0.89[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10800125	PVRL4	cis	parietal	SCAN
rs10800125	SLAMF1	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165603800-165631200	Weak transcription	Fetal Kidney	kidney
2	chr1:165604800-165632200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:165606200-165659600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:165610600-165630800	Weak transcription	Small Intestine	intestine
5	chr1:165615400-165630000	Weak transcription	GM12878-XiMat	blood
6	chr1:165615600-165629600	Weak transcription	Primary B cells from cord blood	blood
7	chr1:165615600-165630200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr1:165615600-165631000	Weak transcription	NHEK	skin
9	chr1:165615800-165631000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:165616400-165630200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:165616400-165632000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:165617000-165630000	Weak transcription	Thymus	Thymus
13	chr1:165617000-165631200	Strong transcription	Fetal Stomach	stomach
14	chr1:165618000-165631000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:165618000-165638600	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:165618200-165652400	Strong transcription	Fetal Muscle Leg	muscle
17	chr1:165618600-165634800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:165618800-165630800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:165618800-165638600	Strong transcription	Fetal Intestine Large	intestine
20	chr1:165619000-165635000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:165619000-165642600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:165619000-165643600	Strong transcription	Fetal Muscle Trunk	muscle
23	chr1:165619200-165630800	Strong transcription	NHDF-Ad	bronchial
24	chr1:165619200-165634200	Strong transcription	Stomach Smooth Muscle	stomach
25	chr1:165619200-165648800	Strong transcription	Liver	Liver
26	chr1:165619400-165636200	Strong transcription	Adipose Nuclei	Adipose
27	chr1:165619600-165642600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:165619600-165653200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:165620800-165631000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:165620800-165631200	Weak transcription	HepG2	liver
31	chr1:165621000-165630800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:165621000-165634400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:165621600-165632200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:165622600-165630600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:165622800-165631200	Weak transcription	A549	lung
36	chr1:165623200-165629200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr1:165623400-165629600	Weak transcription	Esophagus	oesophagus
38	chr1:165623400-165630000	Weak transcription	Fetal Thymus	thymus
39	chr1:165623400-165653000	Weak transcription	Stomach Mucosa	stomach
40	chr1:165623600-165629800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:165623600-165630000	Weak transcription	Primary B cells from peripheral blood	blood
42	chr1:165623800-165629200	Weak transcription	Gastric	stomach
43	chr1:165623800-165631200	Weak transcription	K562	blood
44	chr1:165623800-165631800	Weak transcription	HUVEC	blood vessel
45	chr1:165623800-165636400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr1:165624400-165630800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr1:165624600-165632800	Weak transcription	Colonic Mucosa	Colon
48	chr1:165624800-165629200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:165624800-165631000	Weak transcription	Hela-S3	cervix
50	chr1:165625000-165632200	Weak transcription	Brain Angular Gyrus	brain

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