Variant report

Variant	rs6493776
Chromosome Location	chr15:55571380-55571381
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:55558293..55561051-chr15:55570591..55574257,3	K562	blood:
2	chr15:55527813..55534361-chr15:55567580..55576356,11	K562	blood:
3	chr15:55511874..55516207-chr15:55570260..55572623,4	K562	blood:
4	chr15:55550859..55553459-chr15:55571024..55573794,2	K562	blood:
5	chr15:55561094..55566521-chr15:55568415..55573489,7	K562	blood:
6	chr15:55528399..55531795-chr15:55570084..55572608,4	K562	blood:
7	chr15:55557767..55561627-chr15:55569250..55572425,4	K562	blood:

Variant related genes	Relation type
ENSG00000069974	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11071175	0.84[ASN][1000 genomes]
rs11071177	0.94[ASN][1000 genomes]
rs11635126	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12440730	0.83[ASN][1000 genomes]
rs12595377	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12708446	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12902710	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12902902	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12910733	0.85[ASN][1000 genomes]
rs12912490	0.90[ASN][1000 genomes]
rs2414406	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28459661	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28685005	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28799296	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28852495	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35715239	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4354865	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4558357	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs569333	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs574923	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs678892	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7164608	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7166125	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025833	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8026689	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8032594	0.84[ASN][1000 genomes]
rs8036244	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8036345	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8036729	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8039771	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8040540	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9972478	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042741	chr15:55068022-55622497	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv1036924	chr15:55527874-55616480	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1051046	chr15:55529291-55821973	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv569522	chr15:55532211-55611126	Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv904241	chr15:55534342-55611126	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1036173	chr15:55547689-55812194	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
9	nsv542391	chr15:55547689-55812194	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
10	nsv904242	chr15:55550755-55611126	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv569523	chr15:55555602-55836704	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
12	nsv569524	chr15:55558624-55612511	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
14	nsv531054	chr15:55571230-55914205	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6493776	PIGB	cis	Artery Tibial	GTEx
rs6493776	PIGB	cis	Esophagus Muscularis	GTEx
rs6493776	PIGB	cis	Nerve Tibial	GTEx
rs6493776	PIGB	cis	lung	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55520800-55574800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:55542400-55581000	Weak transcription	Fetal Intestine Small	intestine
3	chr15:55547800-55571400	Weak transcription	Aorta	Aorta
4	chr15:55548600-55574800	Weak transcription	Left Ventricle	heart
5	chr15:55549200-55571600	Weak transcription	HMEC	breast
6	chr15:55550000-55571400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:55553200-55581000	Weak transcription	Fetal Intestine Large	intestine
8	chr15:55560200-55574800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:55560200-55575400	Weak transcription	Thymus	Thymus
10	chr15:55560400-55571800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:55561400-55571400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:55561400-55571400	Weak transcription	Pancreas	Pancrea
13	chr15:55561600-55576600	Weak transcription	Liver	Liver
14	chr15:55563200-55571400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:55563800-55574800	Weak transcription	Lung	lung
16	chr15:55564200-55571400	Weak transcription	Stomach Mucosa	stomach
17	chr15:55565000-55574800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr15:55567200-55572800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr15:55567400-55571800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr15:55567600-55572600	Enhancers	Primary B cells from peripheral blood	blood
21	chr15:55567800-55572600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:55567800-55580800	Weak transcription	Fetal Stomach	stomach
23	chr15:55568400-55574800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:55568600-55572600	Enhancers	Primary hematopoietic stem cells	blood
25	chr15:55569400-55578200	Weak transcription	Fetal Kidney	kidney
26	chr15:55569800-55572600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr15:55569800-55572600	Enhancers	HUVEC	blood vessel
28	chr15:55570000-55571400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr15:55570000-55571400	Weak transcription	Spleen	Spleen
30	chr15:55570000-55571600	Weak transcription	NHLF	lung
31	chr15:55570000-55571800	Weak transcription	Osteobl	bone
32	chr15:55570000-55572600	Enhancers	Primary T cells fromperipheralblood	blood
33	chr15:55570000-55574200	Weak transcription	Right Atrium	heart
34	chr15:55570200-55571400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:55570200-55571400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr15:55570200-55571400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr15:55570200-55571400	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr15:55570200-55571400	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr15:55570200-55571400	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr15:55570200-55571600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr15:55570200-55571800	Weak transcription	Primary T cells from cord blood	blood
42	chr15:55570200-55571800	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr15:55570200-55572000	Weak transcription	Dnd41	blood
44	chr15:55570200-55572600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr15:55570200-55572800	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr15:55570200-55572800	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr15:55570200-55573800	Weak transcription	Gastric	stomach
48	chr15:55570200-55580400	Weak transcription	Fetal Thymus	thymus
49	chr15:55570200-55581200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr15:55570400-55571400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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