Variant report

Variant	rs11548666
Chromosome Location	chr3:150345664-150345665
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	chr3:150341447..150343968-chr3:150345071..150346615,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11921309	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11922033	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924919	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11927175	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11927998	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11929205	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12107730	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16862718	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs17214539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17214746	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17440940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1915945	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1965473	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2030530	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2293150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2293151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55707430	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55723846	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56208302	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56217437	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59885545	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60142519	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61019785	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61667461	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73001317	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73001332	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73001341	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73001347	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73001362	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73001363	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73001365	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73003042	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7430992	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7650013	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv967272	chr3:150340723-150348299	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11548666	SELT	cis	cerebellum	SCAN
rs11548666	SELT	cis	parietal	SCAN
rs11548666	UBQLN4	cis	parietal	SCAN
rs11548666	TM4SF4	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150322200-150347000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:150322400-150350800	Weak transcription	Colonic Mucosa	Colon
3	chr3:150322400-150353000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:150323000-150348200	Weak transcription	Fetal Brain Male	brain
5	chr3:150323000-150348200	Weak transcription	Fetal Lung	lung
6	chr3:150325600-150348400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:150326000-150348400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:150326000-150352800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:150330000-150348800	Weak transcription	Right Ventricle	heart
10	chr3:150330000-150356600	Weak transcription	Gastric	stomach
11	chr3:150330200-150348800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:150330200-150353000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:150330400-150348400	Weak transcription	Fetal Stomach	stomach
14	chr3:150331200-150348800	Weak transcription	Fetal Intestine Small	intestine
15	chr3:150332000-150348600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:150334800-150352800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:150336600-150351200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:150336800-150348400	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:150339800-150353000	Weak transcription	HepG2	liver
20	chr3:150340200-150345800	Strong transcription	Primary hematopoietic stem cells	blood
21	chr3:150340600-150349600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr3:150340800-150345800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr3:150340800-150349800	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr3:150341000-150349400	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:150341000-150349800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:150341200-150345800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr3:150341200-150347000	Strong transcription	HSMM	muscle
28	chr3:150341200-150349000	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:150341200-150349000	Strong transcription	Adipose Nuclei	Adipose
30	chr3:150341200-150349800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:150341200-150350000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr3:150341600-150346000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:150341600-150347600	Strong transcription	Primary B cells from peripheral blood	blood
34	chr3:150341600-150349600	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr3:150341800-150346800	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr3:150341800-150347000	Strong transcription	Primary B cells from cord blood	blood
37	chr3:150341800-150347200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:150341800-150347200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:150341800-150349000	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:150341800-150349400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:150341800-150349600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:150341800-150349600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:150341800-150349800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:150341800-150349800	Strong transcription	Placenta	Placenta
45	chr3:150341800-150349800	Strong transcription	Fetal Thymus	thymus
46	chr3:150342000-150345800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:150342000-150347000	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:150342000-150347000	Strong transcription	HUVEC	blood vessel
49	chr3:150342000-150349600	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:150342200-150347400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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