Variant report

Variant	rs13190784
Chromosome Location	chr6:56733052-56733053
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr6:56733045-56733992	A549	lung:	n/a	chr6:56733655-56733665 chr6:56733655-56733665 chr6:56733275-56733287 chr6:56733277-56733285 chr6:56733655-56733665 chr6:56733103-56733112

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56722965..56725223-chr6:56732847..56735248,2	K562	blood:
2	chr6:56725702..56727982-chr6:56732126..56734324,2	K562	blood:

Variant related genes	Relation type
RPL17P26	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11968575	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs11970648	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs13191084	0.89[EUR][1000 genomes]
rs13191826	0.87[ASN][1000 genomes]
rs13195825	0.99[EUR][1000 genomes]
rs13198597	0.80[CEU][hapmap]
rs13199024	0.99[EUR][1000 genomes]
rs13199233	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13200166	0.88[MEX][hapmap]
rs13200868	0.87[ASN][1000 genomes]
rs13203600	0.98[EUR][1000 genomes]
rs13205022	0.98[EUR][1000 genomes]
rs13207768	0.89[MEX][hapmap];0.81[TSI][hapmap]
rs13209099	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs13215883	0.80[CEU][hapmap]
rs13216793	0.98[EUR][1000 genomes]
rs13218913	0.89[MEX][hapmap]
rs16888171	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs16888186	0.86[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs16888189	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs16888192	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs17684802	0.89[MEX][hapmap]
rs17684878	1.00[MEX][hapmap];0.81[TSI][hapmap]
rs17685045	0.98[EUR][1000 genomes]
rs17752106	0.81[CEU][hapmap]
rs1870638	0.93[CEU][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes]
rs1903332	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs3002010	1.00[CHB][hapmap]
rs3002011	1.00[CHB][hapmap]
rs34966024	0.87[ASN][1000 genomes]
rs35440408	0.87[ASN][1000 genomes]
rs35609883	0.87[ASN][1000 genomes]
rs35886823	0.87[ASN][1000 genomes]
rs4299824	0.89[MEX][hapmap]
rs4415160	0.89[MEX][hapmap]
rs4443500	0.89[EUR][1000 genomes]
rs58980183	0.87[ASN][1000 genomes]
rs60163288	0.87[ASN][1000 genomes]
rs60563401	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61601344	0.87[ASN][1000 genomes]
rs67063738	0.86[EUR][1000 genomes]
rs6904535	0.87[ASN][1000 genomes]
rs6905658	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910414	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6911654	0.89[EUR][1000 genomes]
rs6918949	1.00[MEX][hapmap];0.81[TSI][hapmap]
rs6925518	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926742	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934714	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs71564864	0.99[EUR][1000 genomes]
rs73457800	0.83[EUR][1000 genomes]
rs7744240	0.93[CEU][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs7744799	1.00[CEU][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes]
rs7758867	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs7760542	1.00[CHD][hapmap]
rs7761501	0.89[MEX][hapmap];0.81[TSI][hapmap]
rs7761729	1.00[MEX][hapmap];0.81[TSI][hapmap]
rs9464401	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1022714	chr6:56729767-56826642	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv538229	chr6:56729767-56826642	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13190784	DST	cis	cerebellum	SCAN
rs13190784	RAB23	cis	multi-tissue	Pritchard
rs13190784	BEND6	cis	cerebellum	SCAN
rs13190784	BEND6	cis	parietal	SCAN
rs13190784	BMP5	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56724200-56733800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:56725600-56734800	Enhancers	Hela-S3	cervix
3	chr6:56727200-56734600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:56727600-56734400	Enhancers	HMEC	breast
5	chr6:56727800-56734800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:56728000-56734800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:56728000-56735000	Enhancers	HSMM	muscle
8	chr6:56728000-56735000	Enhancers	NHDF-Ad	bronchial
9	chr6:56728200-56733800	Enhancers	HSMMtube	muscle
10	chr6:56728200-56733800	Enhancers	Osteobl	bone
11	chr6:56728800-56734800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:56730400-56733800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:56730400-56740400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:56731000-56733200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:56731600-56734600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:56731800-56734600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:56731800-56734800	Enhancers	NH-A	brain
18	chr6:56732000-56733400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:56732000-56733400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:56732000-56733800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr6:56732000-56734800	Enhancers	NHLF	lung
22	chr6:56732200-56733200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:56732200-56733600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr6:56732400-56734800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:56732600-56736000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:56732800-56733800	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr6:56732800-56734400	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr6:56733000-56733200	Flanking Active TSS	GM12878-XiMat	blood
29	chr6:56733000-56733400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr6:56733000-56733400	Flanking Active TSS	A549	lung
31	chr6:56733000-56734200	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr6:56733000-56734200	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr6:56733000-56734200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:56733000-56734200	Flanking Active TSS	HUVEC	blood vessel
35	chr6:56733000-56734200	Enhancers	NHEK	skin
36	chr6:56733000-56734400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr6:56733000-56734400	Enhancers	HepG2	liver
38	chr6:56733000-56734600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:56733000-56734800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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