Variant report

Variant	rs9724754
Chromosome Location	chr1:179084408-179084409
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179074516..179077030-chr1:179084166..179086204,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1004959	0.81[ASN][1000 genomes]
rs10157885	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10158768	0.88[ASN][1000 genomes]
rs10913687	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs12066589	0.85[CHB][hapmap]
rs12076957	0.85[CHB][hapmap]
rs12080991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs12143004	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs16853610	0.82[MEX][hapmap]
rs17277358	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17361990	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17362128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017688	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025580	1.00[MEX][hapmap]
rs2274228	0.85[ASN][1000 genomes]
rs2274230	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28459842	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28914474	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28914485	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3753532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766631	0.85[CHB][hapmap]
rs45499094	0.85[ASN][1000 genomes]
rs55642919	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55697941	0.82[AMR][1000 genomes]
rs55825882	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55827544	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55920203	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55955319	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56382583	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60741626	0.86[ASN][1000 genomes]
rs60826716	0.86[ASN][1000 genomes]
rs6668200	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs6669988	0.86[ASN][1000 genomes]
rs9650997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650998	0.97[EUR][1000 genomes]
rs9725888	0.85[CHB][hapmap]
rs9730271	0.88[ASN][1000 genomes]
rs9803885	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002511	chr1:179077914-179089842	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9724754	LAX1	trans	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179053200-179096000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:179059200-179096400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:179059400-179090400	Strong transcription	HUVEC	blood vessel
4	chr1:179061400-179090400	Strong transcription	HSMM	muscle
5	chr1:179062000-179088000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:179063200-179112000	Weak transcription	Fetal Kidney	kidney
7	chr1:179064800-179097800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:179070400-179087200	Weak transcription	Psoas Muscle	Psoas
9	chr1:179071400-179090400	Strong transcription	NHDF-Ad	bronchial
10	chr1:179072000-179090400	Strong transcription	Osteobl	bone
11	chr1:179072200-179090000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:179074200-179088200	Strong transcription	NHEK	skin
13	chr1:179074200-179091000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:179074400-179088200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:179075200-179091200	Strong transcription	NHLF	lung
16	chr1:179075400-179091000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:179075400-179091400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:179075400-179096200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:179075600-179089200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:179075800-179084600	Strong transcription	A549	lung
21	chr1:179075800-179089600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:179076000-179088200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:179076000-179090400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:179076200-179093400	Strong transcription	Fetal Stomach	stomach
25	chr1:179076400-179090400	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr1:179076400-179090400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:179076600-179090000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:179076600-179092800	Strong transcription	NH-A	brain
29	chr1:179076800-179088000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:179077200-179090600	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr1:179077400-179090200	Weak transcription	GM12878-XiMat	blood
32	chr1:179077600-179094000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:179077800-179091000	Strong transcription	Adipose Nuclei	Adipose
34	chr1:179078000-179091200	Strong transcription	HSMMtube	muscle
35	chr1:179078200-179090600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:179078600-179097600	Weak transcription	Stomach Mucosa	stomach
37	chr1:179079600-179086600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:179079600-179109800	Weak transcription	Small Intestine	intestine
39	chr1:179080000-179086000	Weak transcription	Brain Anterior Caudate	brain
40	chr1:179080000-179086000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:179080000-179086000	Weak transcription	Fetal Lung	lung
42	chr1:179080000-179086200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr1:179080000-179086400	Weak transcription	Brain Substantia Nigra	brain
44	chr1:179080000-179087200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr1:179080000-179087400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:179080000-179088000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr1:179080000-179089000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:179080000-179090400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:179080000-179090800	Weak transcription	Fetal Heart	heart
50	chr1:179080000-179090800	Weak transcription	Pancreas	Pancrea

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