Variant report

Variant	rs7168316
Chromosome Location	chr15:49733746-49733747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1023683	0.80[YRI][hapmap]
rs10519226	0.89[LWK][hapmap];0.94[MKK][hapmap];0.89[AFR][1000 genomes]
rs10519227	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11632575	0.83[EUR][1000 genomes]
rs11633282	0.82[EUR][1000 genomes]
rs11635005	0.82[ASW][hapmap]
rs11635308	0.82[ASW][hapmap];0.81[LWK][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11635354	0.86[EUR][1000 genomes]
rs11638314	0.86[EUR][1000 genomes]
rs11638606	0.82[EUR][1000 genomes]
rs12591134	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12591799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12592177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12592277	0.98[GIH][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12592296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12593068	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12593119	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12594154	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12594827	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12595497	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12595701	0.91[ASN][1000 genomes]
rs17396119	0.82[CEU][hapmap]
rs17396536	0.82[CEU][hapmap]
rs17396747	0.82[CEU][hapmap]
rs17397211	0.81[CEU][hapmap]
rs17400427	0.89[AFR][1000 genomes]
rs17400706	0.91[ASW][hapmap];0.82[CEU][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17477722	0.82[ASW][hapmap];0.94[MKK][hapmap];0.84[EUR][1000 genomes]
rs17477923	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17478618	0.91[ASW][hapmap];0.82[CEU][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17479003	0.82[CEU][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17479205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17479289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34635038	0.91[ASN][1000 genomes]
rs3809495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4338740	0.91[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57252806	0.82[EUR][1000 genomes]
rs59112977	0.84[EUR][1000 genomes]
rs60594237	0.80[EUR][1000 genomes]
rs61259878	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7162633	0.82[EUR][1000 genomes]
rs7176697	1.00[CHB][hapmap]
rs73394359	0.80[EUR][1000 genomes]
rs73396235	0.82[EUR][1000 genomes]
rs73396238	0.86[EUR][1000 genomes]
rs73398223	0.82[EUR][1000 genomes]
rs73398243	0.84[EUR][1000 genomes]
rs73398264	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73398272	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73398276	0.86[EUR][1000 genomes]
rs73398284	0.83[AFR][1000 genomes]
rs73400205	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027094	0.84[EUR][1000 genomes]
rs8030457	0.84[EUR][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	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7168316	TNFAIP8L3	cis	parietal	SCAN
rs7168316	CASC4	cis	cerebellum	SCAN
rs7168316	FGF7	cis	Muscle Skeletal	GTEx
rs7168316	SECISBP2L	cis	cerebellum	SCAN
rs7168316	SECISBP2L	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49716400-49737200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr15:49721000-49736200	Weak transcription	Right Ventricle	heart
3	chr15:49725400-49733800	Enhancers	Rectal Smooth Muscle	rectum
4	chr15:49730000-49733800	Enhancers	Primary hematopoietic stem cells	blood
5	chr15:49730400-49744600	Weak transcription	NHLF	lung
6	chr15:49731200-49733800	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr15:49731600-49733800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:49731600-49734600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr15:49731600-49734600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr15:49732000-49736600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:49732000-49750200	Weak transcription	HSMM	muscle
12	chr15:49732200-49736200	Weak transcription	Ovary	ovary
13	chr15:49732200-49736200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr15:49732400-49736800	Weak transcription	Fetal Stomach	stomach
15	chr15:49732400-49738200	Weak transcription	NHDF-Ad	bronchial
16	chr15:49732800-49741000	Weak transcription	Fetal Heart	heart
17	chr15:49733000-49734000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:49733200-49735200	Enhancers	Colon Smooth Muscle	Colon
19	chr15:49733200-49741800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:49733400-49733800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:49733400-49733800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:49733600-49734200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr15:49733600-49734400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:49733600-49734800	Enhancers	Osteobl	bone
25	chr15:49733600-49735200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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