Variant report

Variant	rs12912490
Chromosome Location	chr15:55563495-55563496
allele	G/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	POLR2A	chr15:55562344-55563608	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:55563187..55564952-chr15:55575957..55578942,3	K562	blood:

Variant related genes	Relation type
RAB27A	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11071175	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11071177	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12440730	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12595377	0.90[ASN][1000 genomes]
rs12902710	0.94[CHB][hapmap];0.93[CHD][hapmap]
rs12910733	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs574923	0.94[CHB][hapmap]
rs6493774	0.80[CHB][hapmap];0.83[YRI][hapmap]
rs6493776	0.90[ASN][1000 genomes]
rs678892	0.94[CHB][hapmap];0.90[CHD][hapmap]
rs7166125	0.90[ASN][1000 genomes]
rs8026689	0.94[CHB][hapmap]
rs8032594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8036244	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs8036345	0.94[CHB][hapmap];0.97[CHD][hapmap];0.81[ASN][1000 genomes]
rs8036729	0.87[ASN][1000 genomes]
rs8040540	0.94[CHB][hapmap];0.97[CHD][hapmap]
rs8182068	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs9972478	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12912490	RAB27A	cis	cerebellum	SCAN
rs12912490	PIGB	cis	cerebellum	SCAN
rs12912490	PIGB	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

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	chr15:55559800-55569400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:55559800-55571200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr15:55560000-55566200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr15:55560200-55567400	Weak transcription	Gastric	stomach
12	chr15:55560200-55569800	Weak transcription	Hela-S3	cervix
13	chr15:55560200-55571200	Weak transcription	NHDF-Ad	bronchial
14	chr15:55560200-55574800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:55560200-55575400	Weak transcription	Thymus	Thymus
16	chr15:55560400-55564600	Enhancers	Primary T cells fromperipheralblood	blood
17	chr15:55560400-55565000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr15:55560400-55568600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr15:55560400-55571800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:55560600-55565200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr15:55560600-55568200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr15:55560600-55569000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:55560600-55569600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr15:55560600-55569600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:55560800-55563600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr15:55560800-55565200	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr15:55560800-55567600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr15:55560800-55569400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:55561000-55563600	Genic enhancers	Primary monocytes fromperipheralblood	blood
30	chr15:55561000-55563800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:55561000-55567600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr15:55561200-55568600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr15:55561400-55565000	Weak transcription	K562	blood
34	chr15:55561400-55567400	Weak transcription	Primary B cells from cord blood	blood
35	chr15:55561400-55571400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:55561400-55571400	Weak transcription	Pancreas	Pancrea
37	chr15:55561600-55576600	Weak transcription	Liver	Liver
38	chr15:55562400-55569600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:55562600-55564200	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr15:55562800-55563600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr15:55562800-55564200	Enhancers	Stomach Mucosa	stomach
42	chr15:55562800-55567200	Weak transcription	Fetal Stomach	stomach
43	chr15:55562800-55569400	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr15:55563000-55567400	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr15:55563200-55563600	Weak transcription	Lung	lung
46	chr15:55563200-55571400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr15:55563400-55563800	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr15:55563400-55564000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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