Variant report

Variant	rs11921309
Chromosome Location	chr3:150255385-150255386
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11548666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11922033	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11924919	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11927175	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11927998	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11929205	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12107730	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17214539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17214746	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs17440940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1915945	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965473	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2030530	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55707430	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55723846	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56208302	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56217437	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59885545	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60142519	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61019785	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61667461	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73001317	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73001332	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73001341	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73001347	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73001362	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73001363	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73001365	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73003042	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7430992	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650013	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11921309	TM4SF4	cis	parietal	SCAN
rs11921309	UBQLN4	cis	parietal	SCAN
rs11921309	SELT	cis	parietal	SCAN
rs11921309	SELT	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150235400-150256600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:150246200-150260600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr3:150246400-150259000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:150246400-150259200	Weak transcription	Fetal Lung	lung
5	chr3:150246400-150261800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:150246400-150262600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:150247000-150259400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:150248400-150263200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:150248800-150262000	Weak transcription	Thymus	Thymus
10	chr3:150249600-150260400	Weak transcription	GM12878-XiMat	blood
11	chr3:150251200-150259400	Weak transcription	Fetal Brain Female	brain
12	chr3:150252600-150259000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:150252600-150259000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:150253200-150259000	Weak transcription	HSMMtube	muscle
15	chr3:150253400-150258800	Weak transcription	A549	lung
16	chr3:150253400-150259200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:150253400-150259600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:150253600-150255800	Weak transcription	Stomach Mucosa	stomach
19	chr3:150254000-150259200	Weak transcription	HSMM	muscle
20	chr3:150254400-150259200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:150254400-150262000	Weak transcription	Fetal Intestine Small	intestine
22	chr3:150254400-150262600	Weak transcription	Fetal Stomach	stomach
23	chr3:150254800-150259200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:150254800-150259400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:150254800-150259400	Weak transcription	Hela-S3	cervix
26	chr3:150254800-150261400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:150255000-150259200	Weak transcription	Primary B cells from cord blood	blood
28	chr3:150255000-150261000	Weak transcription	Fetal Brain Male	brain
29	chr3:150255200-150259800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr3:150255200-150260600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:150255200-150262600	Weak transcription	Right Ventricle	heart

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