Variant report

Variant	rs1274439
Chromosome Location	chr10:92483812-92483813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10509609	0.81[CEU][hapmap]
rs11592512	0.81[CEU][hapmap]
rs1274444	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1296196	0.80[CEU][hapmap]
rs1419355	0.97[ASN][1000 genomes]
rs1857586	0.98[ASN][1000 genomes]
rs1936620	0.98[ASN][1000 genomes]
rs1936621	0.98[ASN][1000 genomes]
rs1936623	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2154134	0.96[ASN][1000 genomes]
rs2710721	0.91[ASN][1000 genomes]
rs2710723	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2800134	0.99[ASN][1000 genomes]
rs2800135	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2800136	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2800137	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2800138	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2800139	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3740046	0.81[CEU][hapmap]
rs7904560	0.93[CEU][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422237	chr10:91940542-92547558	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1052753	chr10:92081093-92565617	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv467432	chr10:92082250-92559908	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv551879	chr10:92082250-92559908	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv467433	chr10:92083015-92598458	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv551880	chr10:92083015-92598458	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv516743	chr10:92083015-92605119	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1049931	chr10:92083932-92605364	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv948363	chr10:92084520-92614402	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv551882	chr10:92090785-92598823	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv1047255	chr10:92095431-92548184	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv540744	chr10:92095431-92548184	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1054504	chr10:92099335-92590723	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv533133	chr10:92363552-92594891	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv1036058	chr10:92471568-92605364	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1274439	PTEN	cis	cerebellum	SCAN
rs1274439	LIPK	cis	parietal	SCAN
rs1274439	FAS	cis	cerebellum	SCAN
rs1274439	FLJ37201	cis	parietal	SCAN
rs1274439	LIPK	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:92482600-92484200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr10:92482600-92484200	Enhancers	Primary T cells fromperipheralblood	blood
3	chr10:92482600-92484400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr10:92482600-92484400	Enhancers	Fetal Thymus	thymus
5	chr10:92482600-92485000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr10:92482600-92485800	Enhancers	H1 Cell Line	embryonic stem cell
7	chr10:92482800-92484000	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr10:92482800-92484000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr10:92482800-92484200	Enhancers	Primary T cells from cord blood	blood
10	chr10:92482800-92485800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr10:92482800-92486000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr10:92482800-92486400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr10:92483000-92486000	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr10:92483000-92486000	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr10:92483200-92484000	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr10:92483200-92484200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr10:92483200-92484200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr10:92483200-92484200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr10:92483200-92484200	Enhancers	NHEK	skin
20	chr10:92483200-92484400	Enhancers	H9 Cell Line	embryonic stem cell
21	chr10:92483200-92484400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr10:92483200-92484400	Enhancers	HMEC	breast
23	chr10:92483200-92486200	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr10:92483600-92486000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr10:92483800-92484000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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