Variant report

Variant	rs17277358
Chromosome Location	chr1:179100710-179100711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179095025..179097028-chr1:179098926..179100910,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

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]
rs11808217	1.00[JPT][hapmap]
rs12066589	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12071751	1.00[JPT][hapmap]
rs12076957	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12080991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs12083856	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs12143004	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16853610	0.87[TSI][hapmap]
rs16853619	0.89[CHD][hapmap]
rs17361990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17362128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017688	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025580	1.00[MEX][hapmap];0.87[TSI][hapmap]
rs2274228	0.85[ASN][1000 genomes]
rs2274230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.88[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	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28914485	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3753532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766631	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs3766633	1.00[JPT][hapmap]
rs3766634	1.00[JPT][hapmap]
rs45499094	0.85[ASN][1000 genomes]
rs55642919	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55825882	0.94[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	0.94[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	0.94[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];0.88[TSI][hapmap];0.97[EUR][1000 genomes]
rs6669988	0.86[ASN][1000 genomes]
rs7516491	1.00[JPT][hapmap];0.87[TSI][hapmap]
rs9650997	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650998	0.97[EUR][1000 genomes]
rs9724754	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]
rs9725888	0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs9726948	1.00[JPT][hapmap]
rs9730271	0.88[ASN][1000 genomes]
rs9803885	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012667	chr1:179094571-179120280	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1002253	chr1:179094571-179120938	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1001191	chr1:179097246-179120938	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17277358	LAX1	trans	lymphoblastoid	seeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179063200-179112000	Weak transcription	Fetal Kidney	kidney
2	chr1:179079600-179109800	Weak transcription	Small Intestine	intestine
3	chr1:179080200-179101600	Weak transcription	Fetal Brain Male	brain
4	chr1:179080400-179103800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:179086600-179105000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:179087800-179113000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:179088200-179102400	Weak transcription	Brain Germinal Matrix	brain
8	chr1:179090800-179104400	Weak transcription	Fetal Brain Female	brain
9	chr1:179091000-179108800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:179091000-179109000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:179091000-179109200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:179093400-179117200	Weak transcription	Fetal Stomach	stomach
13	chr1:179095600-179101000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:179095800-179100800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:179095800-179101800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:179095800-179103600	Weak transcription	Fetal Intestine Large	intestine
17	chr1:179095800-179106800	Weak transcription	Gastric	stomach
18	chr1:179095800-179107400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:179096400-179108800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:179096600-179106800	Weak transcription	Fetal Lung	lung
21	chr1:179096600-179110200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:179097000-179101600	Genic enhancers	HUVEC	blood vessel
23	chr1:179098200-179112000	Weak transcription	Lung	lung
24	chr1:179098400-179101000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:179098600-179100800	Strong transcription	HSMMtube	muscle
26	chr1:179098800-179101000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:179098800-179101000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:179099000-179100800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:179099200-179100800	Strong transcription	Fetal Muscle Trunk	muscle
30	chr1:179099200-179100800	Genic enhancers	NHDF-Ad	bronchial
31	chr1:179099200-179101000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:179099200-179101200	Genic enhancers	HSMM	muscle
33	chr1:179099200-179110200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr1:179099200-179110400	Weak transcription	Brain Angular Gyrus	brain
35	chr1:179099200-179110400	Weak transcription	Brain Anterior Caudate	brain
36	chr1:179099200-179114800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr1:179099400-179100800	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:179099400-179100800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:179099400-179100800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:179099400-179101000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:179099400-179101000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:179099400-179101600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:179099400-179103400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:179099400-179106800	Weak transcription	Pancreas	Pancrea
45	chr1:179099400-179106800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr1:179099400-179106800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr1:179099400-179107000	Weak transcription	Placenta	Placenta
48	chr1:179099400-179110000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:179099400-179110400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:179099400-179112000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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